| 1 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> |
|---|
| 2 | <!-- |
|---|
| 3 | $Id: index.html 4783 2009-02-23 13:54:13Z nicklas $ |
|---|
| 4 | |
|---|
| 5 | Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Martin Svensson |
|---|
| 6 | |
|---|
| 7 | This file is part of BASE - BioArray Software Environment. |
|---|
| 8 | Available at http://base.thep.lu.se/ |
|---|
| 9 | |
|---|
| 10 | BASE is free software; you can redistribute it and/or |
|---|
| 11 | modify it under the terms of the GNU General Public License |
|---|
| 12 | as published by the Free Software Foundation; either version 3 |
|---|
| 13 | of the License, or (at your option) any later version. |
|---|
| 14 | |
|---|
| 15 | BASE is distributed in the hope that it will be useful, |
|---|
| 16 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
|---|
| 17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|---|
| 18 | GNU General Public License for more details. |
|---|
| 19 | |
|---|
| 20 | You should have received a copy of the GNU General Public License |
|---|
| 21 | along with BASE. If not, see <http://www.gnu.org/licenses/>. |
|---|
| 22 | --> |
|---|
| 23 | <html> |
|---|
| 24 | <head> |
|---|
| 25 | <title>BASE - Test procedures for predefined roles</title> |
|---|
| 26 | <link rel=stylesheet type="text/css" href="../../historical/styles.css"> |
|---|
| 27 | </head> |
|---|
| 28 | <body> |
|---|
| 29 | |
|---|
| 30 | <div class="navigation"> |
|---|
| 31 | <a href="../../index.html">BASE</a> |
|---|
| 32 | <img src="../../next.gif"> |
|---|
| 33 | <a href="../index.html">Test procedures</a> |
|---|
| 34 | <img src="../../next.gif"> |
|---|
| 35 | Predefined roles |
|---|
| 36 | </div> |
|---|
| 37 | |
|---|
| 38 | <h1>Test procedures for predefined roles</h1> |
|---|
| 39 | |
|---|
| 40 | <div class="abstract"> |
|---|
| 41 | <p> |
|---|
| 42 | This document defines a procedure for testing that |
|---|
| 43 | the predefined roles can perform their work as intended. The main |
|---|
| 44 | purpose is to weed out permission problems resulting from: |
|---|
| 45 | </p> |
|---|
| 46 | |
|---|
| 47 | <ul> |
|---|
| 48 | <li>Incorrect permissions installed by installation program</li> |
|---|
| 49 | <li>Bugs in the permission handling in the core</li> |
|---|
| 50 | <li>Incorrect handling of permissions in the web client</li> |
|---|
| 51 | </ul> |
|---|
| 52 | |
|---|
| 53 | <p> |
|---|
| 54 | The test procedure also tests that the |
|---|
| 55 | basic functionality is working: |
|---|
| 56 | </p> |
|---|
| 57 | |
|---|
| 58 | <ul> |
|---|
| 59 | <li>Creating items and linking them to other items</li> |
|---|
| 60 | <li>Defining import file formats</li> |
|---|
| 61 | <li>Importing array LIMS data</li> |
|---|
| 62 | <li>Importing and validating raw data against array LIMS data</li> |
|---|
| 63 | <li>Running analysis plug-ins</li> |
|---|
| 64 | <li>Using files instead of the database for storing data</li> |
|---|
| 65 | </ul> |
|---|
| 66 | |
|---|
| 67 | <b>Contents</b><br> |
|---|
| 68 | <ol> |
|---|
| 69 | <li><a href="#summary">Summary of the test procedure</a></li> |
|---|
| 70 | <li><a href="#root">Root user tests</a></li> |
|---|
| 71 | <li><a href="#admin">Administrator tests</a></li> |
|---|
| 72 | <li><a href="#power">Power user tests</a></li> |
|---|
| 73 | <li><a href="#user">User tests</a></li> |
|---|
| 74 | <li><a href="#analysis">Analysis tests</a></li> |
|---|
| 75 | </ol> |
|---|
| 76 | |
|---|
| 77 | <p class="authors"> |
|---|
| 78 | <b>Last updated:</b> $Date: 2009-02-23 13:54:13 +0000 (Mon, 23 Feb 2009) $ |
|---|
| 79 | </p> |
|---|
| 80 | </div> |
|---|
| 81 | |
|---|
| 82 | |
|---|
| 83 | <a name="summary"></a> |
|---|
| 84 | <h2>1. Summary of the test procedure</h2> |
|---|
| 85 | |
|---|
| 86 | <p> |
|---|
| 87 | Here is a summary of the test procedure: |
|---|
| 88 | </p> |
|---|
| 89 | |
|---|
| 90 | <ol> |
|---|
| 91 | <li>Always start with a fresh installation.</li> |
|---|
| 92 | |
|---|
| 93 | <li>The root user creates an administrator.</li> |
|---|
| 94 | |
|---|
| 95 | <li>The administrator creates more users and some global resources: |
|---|
| 96 | <ul> |
|---|
| 97 | <li>A group and three other users. One power user, one user and one guest.</li> |
|---|
| 98 | <li>File formats for importing reporters</li> |
|---|
| 99 | <li>Imports reporters</li> |
|---|
| 100 | </ul> |
|---|
| 101 | </li> |
|---|
| 102 | |
|---|
| 103 | <li>The power user creates item related to the project management: |
|---|
| 104 | <ul> |
|---|
| 105 | <li>A project</li> |
|---|
| 106 | <li>Protocols, one for each type of action: sampling, extraction, etc.</li> |
|---|
| 107 | <li>Hardware and software that are used in the project</li> |
|---|
| 108 | <li>Annotation types for annotations used in the project</li> |
|---|
| 109 | <li>File formats for importing plates, print maps and raw data</li> |
|---|
| 110 | <li>LIMS information - plate type, plates, array design, array batch and array slides</li> |
|---|
| 111 | </ul> |
|---|
| 112 | </li> |
|---|
| 113 | |
|---|
| 114 | <li>The user creates items related to an actual experiment: |
|---|
| 115 | <ul> |
|---|
| 116 | <li>Biomaterials: biosources, samples, extracts, etc.</li> |
|---|
| 117 | <li>Experiment: hybridizations, scans, images, raw bioassays</li> |
|---|
| 118 | <li>Import raw data</li> |
|---|
| 119 | </ul> |
|---|
| 120 | </li> |
|---|
| 121 | |
|---|
| 122 | <li>Both the user and the guest then do some analysis: |
|---|
| 123 | <ul> |
|---|
| 124 | <li>Create a root bioassay set</li> |
|---|
| 125 | <li>Filter the bioassay set</li> |
|---|
| 126 | <li>Run a normalization plug-in</li> |
|---|
| 127 | <li>Check the result by listing and plotting the data</li> |
|---|
| 128 | </ul> |
|---|
| 129 | </li> |
|---|
| 130 | </ol> |
|---|
| 131 | |
|---|
| 132 | <p> |
|---|
| 133 | These tests can also be run in automated mode by test programs. This will of |
|---|
| 134 | course not test the web client, but are useful if one quickly needs to do |
|---|
| 135 | parts of the test and then continue with, for example, the user or analysis tests |
|---|
| 136 | on the web. |
|---|
| 137 | </p> |
|---|
| 138 | |
|---|
| 139 | <p> |
|---|
| 140 | The data files needed by the tests are NOT included in the subversion repository. |
|---|
| 141 | The main reason is that they are too large, and that we don't have permission to |
|---|
| 142 | make them publicly available for download. To get the test file you need to be a |
|---|
| 143 | core developer. Read the instructions on the |
|---|
| 144 | <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a> |
|---|
| 145 | page, <code>Test data</code> section on the Base 2 web site. The automated |
|---|
| 146 | test programs require that file are placed (checked out) in the 'testdata' |
|---|
| 147 | directory located in the BASE root directory. NOTE! Some test data files are |
|---|
| 148 | bzip-compressed. These need to be uncompressed before they are uploaded to BASE. |
|---|
| 149 | </p> |
|---|
| 150 | |
|---|
| 151 | <p> |
|---|
| 152 | To run the tests do the following: |
|---|
| 153 | </p> |
|---|
| 154 | <ol> |
|---|
| 155 | |
|---|
| 156 | <li>Compile the core and the test programs: <code>ant main test</code>.</li> |
|---|
| 157 | |
|---|
| 158 | <li>Change to the <code>build/test/</code> directory.</li> |
|---|
| 159 | |
|---|
| 160 | <li>Run test programs: <code>./test.sh roles [OPTION] <cmds></code> where |
|---|
| 161 | <code><cmds></code> is one or more of the following: |
|---|
| 162 | <ul> |
|---|
| 163 | <li><code>all</code>: run all tests</li> |
|---|
| 164 | <li><code>root</code>: run the root user tests</li> |
|---|
| 165 | <li><code>admin</code>: run the administrator tests</li> |
|---|
| 166 | <li><code>power</code>: run the power user tests</li> |
|---|
| 167 | <li><code>user</code>: run the regular user tests</li> |
|---|
| 168 | <li><code>guest</code>: run the guest user tests</li> |
|---|
| 169 | </ul> |
|---|
| 170 | and <code>OPTION</code> can be none or more of: |
|---|
| 171 | <ul> |
|---|
| 172 | <li><code>-b</code>: if the batch importers should be tested</li> |
|---|
| 173 | <li><code>-w</code>: if the test program should wait for ENTER before emptying the database.</li> |
|---|
| 174 | </ul> |
|---|
| 175 | </li> |
|---|
| 176 | |
|---|
| 177 | </ol> |
|---|
| 178 | |
|---|
| 179 | <a name="root"></a> |
|---|
| 180 | <h2>2. Root user tests</h2> |
|---|
| 181 | <p> |
|---|
| 182 | The root user creates an administrator which is a server-wide admin. |
|---|
| 183 | </p> |
|---|
| 184 | |
|---|
| 185 | <ol> |
|---|
| 186 | <li> |
|---|
| 187 | Create a new user and set the following |
|---|
| 188 | properties. All other properties may remain unchanged. |
|---|
| 189 | |
|---|
| 190 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 191 | <tr> |
|---|
| 192 | <th>Name</th> |
|---|
| 193 | <th>Login/Password</th> |
|---|
| 194 | <th>Quota</th> |
|---|
| 195 | <th>Quota group</th> |
|---|
| 196 | <th>Membership</th> |
|---|
| 197 | </tr> |
|---|
| 198 | <tr> |
|---|
| 199 | <td>Admin</td> |
|---|
| 200 | <td>admin/admin</td> |
|---|
| 201 | <td>Unlimited</td> |
|---|
| 202 | <td>-</td> |
|---|
| 203 | <td>Roles: Administrator</td> |
|---|
| 204 | </tr> |
|---|
| 205 | </table> |
|---|
| 206 | </li> |
|---|
| 207 | </ol> |
|---|
| 208 | |
|---|
| 209 | <a name="admin"></a> |
|---|
| 210 | <h2>3. Administrator tests</h2> |
|---|
| 211 | <p> |
|---|
| 212 | The administrator creates users for a project and gives them permissions |
|---|
| 213 | that are suitable for their role in the project. The administrator also |
|---|
| 214 | sets up quota and group membership. |
|---|
| 215 | </p> |
|---|
| 216 | |
|---|
| 217 | <ol> |
|---|
| 218 | <li> |
|---|
| 219 | Create a new group and set the following properties: |
|---|
| 220 | |
|---|
| 221 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 222 | <tr> |
|---|
| 223 | <th>Name</th> |
|---|
| 224 | <th>Quota</th> |
|---|
| 225 | </tr> |
|---|
| 226 | <tr> |
|---|
| 227 | <td>Group A</td> |
|---|
| 228 | <td>1GB</td> |
|---|
| 229 | </tr> |
|---|
| 230 | </table> |
|---|
| 231 | <p> |
|---|
| 232 | </li> |
|---|
| 233 | |
|---|
| 234 | <li> |
|---|
| 235 | Create the following users: |
|---|
| 236 | |
|---|
| 237 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 238 | <tr> |
|---|
| 239 | <th>Name</th> |
|---|
| 240 | <th>Login/Password</th> |
|---|
| 241 | <th>Quota</th> |
|---|
| 242 | <th>Quota group</th> |
|---|
| 243 | <th>Membership</th> |
|---|
| 244 | <th>Other</th> |
|---|
| 245 | </tr> |
|---|
| 246 | <tr> |
|---|
| 247 | <td>Power user</td> |
|---|
| 248 | <td>power/power</td> |
|---|
| 249 | <td>1GB</td> |
|---|
| 250 | <td>Group A</td> |
|---|
| 251 | <td>Roles: Power user</td> |
|---|
| 252 | <td>-</td> |
|---|
| 253 | </tr> |
|---|
| 254 | <tr> |
|---|
| 255 | <td>User</td> |
|---|
| 256 | <td>user/user</td> |
|---|
| 257 | <td>1GB</td> |
|---|
| 258 | <td>Group A</td> |
|---|
| 259 | <td>Roles: User</td> |
|---|
| 260 | <td>-</td> |
|---|
| 261 | </tr> |
|---|
| 262 | <tr> |
|---|
| 263 | <td>Guest</td> |
|---|
| 264 | <td>guest/guest</td> |
|---|
| 265 | <td>10MB</td> |
|---|
| 266 | <td>Group A</td> |
|---|
| 267 | <td>Roles: Guest</td> |
|---|
| 268 | <td><i>Multi-user account</i> checked</td> |
|---|
| 269 | </tr> |
|---|
| 270 | </table> |
|---|
| 271 | <p> |
|---|
| 272 | </li> |
|---|
| 273 | |
|---|
| 274 | <li>Give USE permission for the listed users to the following plugins: |
|---|
| 275 | |
|---|
| 276 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 277 | <tr> |
|---|
| 278 | <th>User</th> |
|---|
| 279 | <th>Plugins</th> |
|---|
| 280 | </tr> |
|---|
| 281 | <tr> |
|---|
| 282 | <td>Power user</td> |
|---|
| 283 | <td> |
|---|
| 284 | <ul> |
|---|
| 285 | <li>Plate importer</li> |
|---|
| 286 | <li>Reporter map importer</li> |
|---|
| 287 | <li>Print map importer</li> |
|---|
| 288 | <li>Array design importer</li> |
|---|
| 289 | <li>Array batch importer</li> |
|---|
| 290 | <li>Array slide importer</li> |
|---|
| 291 | </ul> |
|---|
| 292 | </td> |
|---|
| 293 | </tr> |
|---|
| 294 | </table> |
|---|
| 295 | <p> |
|---|
| 296 | </li> |
|---|
| 297 | |
|---|
| 298 | <li> |
|---|
| 299 | Create file formats (<i>i.e.</i>, plug-in configurations) for importing |
|---|
| 300 | reporters. The formats marked as |
|---|
| 301 | optional are not used in the test procedure, but may be useful to weed |
|---|
| 302 | out import problems, since they allow importing all info from the raw |
|---|
| 303 | data files. You may either enter the regular expressions as specified or |
|---|
| 304 | use the "Test with file" feature. |
|---|
| 305 | |
|---|
| 306 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 307 | <tr> |
|---|
| 308 | <th>Name</th> |
|---|
| 309 | <th>Plugin</th> |
|---|
| 310 | <th>Configuration values</th> |
|---|
| 311 | </tr> |
|---|
| 312 | <tr class="oddrow"> |
|---|
| 313 | <td>Reporters for project A</td> |
|---|
| 314 | <td>Reporter importer</td> |
|---|
| 315 | <td> |
|---|
| 316 | <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code> |
|---|
| 317 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 318 | <tr> |
|---|
| 319 | <td><i>Data header</i></td> |
|---|
| 320 | <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td> |
|---|
| 321 | </tr> |
|---|
| 322 | <tr> |
|---|
| 323 | <td><i>Data splitter</i></td> |
|---|
| 324 | <td>\t</td> |
|---|
| 325 | </tr> |
|---|
| 326 | <tr> |
|---|
| 327 | <td><i>Min data columns</i></td> |
|---|
| 328 | <td>5</td> |
|---|
| 329 | </tr> |
|---|
| 330 | <tr> |
|---|
| 331 | <td><i>Name</i></td> |
|---|
| 332 | <td>\oligo_id\</td> |
|---|
| 333 | </tr> |
|---|
| 334 | <tr> |
|---|
| 335 | <td><i>External ID</i></td> |
|---|
| 336 | <td>\oligo_id\</td> |
|---|
| 337 | </tr> |
|---|
| 338 | <tr> |
|---|
| 339 | <td><i>Description</i></td> |
|---|
| 340 | <td>\description_Ensembl*\</td> |
|---|
| 341 | </tr> |
|---|
| 342 | <tr> |
|---|
| 343 | <td><i>Gene symbol</i></td> |
|---|
| 344 | <td>\gene_symbol_Ensembl*\</td> |
|---|
| 345 | </tr> |
|---|
| 346 | <tr> |
|---|
| 347 | <td><i>Sequence</i></td> |
|---|
| 348 | <td>\oligo_sequence\</td> |
|---|
| 349 | </tr> |
|---|
| 350 | </table> |
|---|
| 351 | |
|---|
| 352 | </td> |
|---|
| 353 | </tr> |
|---|
| 354 | |
|---|
| 355 | <tr class="evenrow"> |
|---|
| 356 | <td>GenePix reporter importer<br>(optional)</td> |
|---|
| 357 | <td>Reporter importer</td> |
|---|
| 358 | <td> |
|---|
| 359 | |
|---|
| 360 | <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code> |
|---|
| 361 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 362 | <tr> |
|---|
| 363 | <td><i>Data header</i></td> |
|---|
| 364 | <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td> |
|---|
| 365 | </tr> |
|---|
| 366 | <tr> |
|---|
| 367 | <td><i>Data splitter</i></td> |
|---|
| 368 | <td>\t</td> |
|---|
| 369 | </tr> |
|---|
| 370 | <tr> |
|---|
| 371 | <td><i>Min data columns</i></td> |
|---|
| 372 | <td>48</td> |
|---|
| 373 | </tr> |
|---|
| 374 | <tr> |
|---|
| 375 | <td><i>Max data columns</i></td> |
|---|
| 376 | <td>48</td> |
|---|
| 377 | </tr> |
|---|
| 378 | <tr> |
|---|
| 379 | <td><i>Name</i></td> |
|---|
| 380 | <td>\Name\</td> |
|---|
| 381 | </tr> |
|---|
| 382 | <tr> |
|---|
| 383 | <td><i>External ID</i></td> |
|---|
| 384 | <td>\ID\</td> |
|---|
| 385 | </tr> |
|---|
| 386 | </table> |
|---|
| 387 | |
|---|
| 388 | </td> |
|---|
| 389 | </tr> |
|---|
| 390 | <tr class="oddrow"> |
|---|
| 391 | <td>Reporters from Affymetrix annotations file</td> |
|---|
| 392 | <td>Reporter importer</td> |
|---|
| 393 | <td> |
|---|
| 394 | <b>Test with file:</b> <code>MG_U74Av2_annot.csv.bz2</code> |
|---|
| 395 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 396 | <tr> |
|---|
| 397 | <td><i>Data header</i></td> |
|---|
| 398 | <td>"Probe Set ID","GeneChip Array".*</td> |
|---|
| 399 | </tr> |
|---|
| 400 | <tr> |
|---|
| 401 | <td><i>Data splitter</i></td> |
|---|
| 402 | <td>(?!"),(?=")</td> |
|---|
| 403 | </tr> |
|---|
| 404 | <tr> |
|---|
| 405 | <td><i>Name</i></td> |
|---|
| 406 | <td>\Probe Set ID\</td> |
|---|
| 407 | </tr> |
|---|
| 408 | <tr> |
|---|
| 409 | <td><i>External ID</i></td> |
|---|
| 410 | <td>\Probe Set ID\</td> |
|---|
| 411 | </tr> |
|---|
| 412 | <tr> |
|---|
| 413 | <td><i>Description</i></td> |
|---|
| 414 | <td>\Target Description\</td> |
|---|
| 415 | </tr> |
|---|
| 416 | <tr> |
|---|
| 417 | <td><i>Gene symbol</i></td> |
|---|
| 418 | <td>\Gene Symbol\</td> |
|---|
| 419 | </tr> |
|---|
| 420 | </table> |
|---|
| 421 | |
|---|
| 422 | </td> |
|---|
| 423 | </tr> |
|---|
| 424 | </table> |
|---|
| 425 | <p> |
|---|
| 426 | </li> |
|---|
| 427 | |
|---|
| 428 | <li> |
|---|
| 429 | Import reporters: |
|---|
| 430 | <ol> |
|---|
| 431 | <li>Go to the <code>View -> Reporters</code> page.</li> |
|---|
| 432 | <li>Click on the <code>Import</code> button.</li> |
|---|
| 433 | <li>Choose <code>auto-detect</code> and then upload |
|---|
| 434 | the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li> |
|---|
| 435 | <li>The <code>Reporters for project A</code> format should be |
|---|
| 436 | found.</li> |
|---|
| 437 | <li>Select the <code>skip</code> option for the "Missing a required" value |
|---|
| 438 | since the file contains rows with empty reporter ID:s. |
|---|
| 439 | <li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li> |
|---|
| 440 | <li> |
|---|
| 441 | Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time |
|---|
| 442 | also select <code>crop</code> for the "String too long" setting since |
|---|
| 443 | the file contains data that is too large for the datbase. |
|---|
| 444 | 12,488 new reporters should be created. |
|---|
| 445 | </ol> |
|---|
| 446 | <p> |
|---|
| 447 | |
|---|
| 448 | </li> |
|---|
| 449 | |
|---|
| 450 | |
|---|
| 451 | </ol> |
|---|
| 452 | |
|---|
| 453 | |
|---|
| 454 | <a name="power"></a> |
|---|
| 455 | <h2>4. Power user tests</h2> |
|---|
| 456 | <p> |
|---|
| 457 | The power user is the typical owner/administrator of a project. The power user sets |
|---|
| 458 | up common resources used in the project, such as hardware, software, protocols, |
|---|
| 459 | file formats and annotation types. In this case the power user is also responsible for |
|---|
| 460 | managing the LIMS. |
|---|
| 461 | </p> |
|---|
| 462 | |
|---|
| 463 | <ol> |
|---|
| 464 | <li> |
|---|
| 465 | Create a project: |
|---|
| 466 | |
|---|
| 467 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 468 | <tr> |
|---|
| 469 | <th>Name</th> |
|---|
| 470 | <th>Members</th> |
|---|
| 471 | </tr> |
|---|
| 472 | <tr> |
|---|
| 473 | <td>Project A</td> |
|---|
| 474 | <td>Groups: Group A (Use permission)</td> |
|---|
| 475 | </tr> |
|---|
| 476 | </table> |
|---|
| 477 | <p> |
|---|
| 478 | </li> |
|---|
| 479 | |
|---|
| 480 | <li>Activate the project.<p></li> |
|---|
| 481 | |
|---|
| 482 | <li> |
|---|
| 483 | Create protocols: |
|---|
| 484 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 485 | <tr> |
|---|
| 486 | <th>Name</th> |
|---|
| 487 | <th>Type</th> |
|---|
| 488 | </tr> |
|---|
| 489 | <tr> |
|---|
| 490 | <td>Sampling A</td> |
|---|
| 491 | <td>Sampling</td> |
|---|
| 492 | </tr> |
|---|
| 493 | <tr> |
|---|
| 494 | <td>Extraction A</td> |
|---|
| 495 | <td>Extraction</td> |
|---|
| 496 | </tr> |
|---|
| 497 | <tr> |
|---|
| 498 | <td>Labeling A</td> |
|---|
| 499 | <td>Labeling</td> |
|---|
| 500 | </tr> |
|---|
| 501 | <tr> |
|---|
| 502 | <td>Hybridization A</td> |
|---|
| 503 | <td>Hybridization</td> |
|---|
| 504 | </tr> |
|---|
| 505 | <tr> |
|---|
| 506 | <td>Scanning A</td> |
|---|
| 507 | <td>Scanning</td> |
|---|
| 508 | </tr> |
|---|
| 509 | <tr> |
|---|
| 510 | <td>Feature extraction A</td> |
|---|
| 511 | <td>Feature extraction</td> |
|---|
| 512 | </tr> |
|---|
| 513 | <tr> |
|---|
| 514 | <td>Printing A</td> |
|---|
| 515 | <td>Printing</td> |
|---|
| 516 | </tr> |
|---|
| 517 | </table> |
|---|
| 518 | <p> |
|---|
| 519 | </li> |
|---|
| 520 | |
|---|
| 521 | <li> |
|---|
| 522 | Create hardware: |
|---|
| 523 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 524 | <tr> |
|---|
| 525 | <th>Name</th> |
|---|
| 526 | <th>Type</th> |
|---|
| 527 | </tr> |
|---|
| 528 | <tr> |
|---|
| 529 | <td>Hybridization station A</td> |
|---|
| 530 | <td>Hybridization station</td> |
|---|
| 531 | </tr> |
|---|
| 532 | <tr> |
|---|
| 533 | <td>Scanner A</td> |
|---|
| 534 | <td>Scanner</td> |
|---|
| 535 | </tr> |
|---|
| 536 | <tr> |
|---|
| 537 | <td>Print robot A</td> |
|---|
| 538 | <td>Print robot</td> |
|---|
| 539 | </tr> |
|---|
| 540 | </table> |
|---|
| 541 | <p> |
|---|
| 542 | </li> |
|---|
| 543 | |
|---|
| 544 | <li> |
|---|
| 545 | Create software: |
|---|
| 546 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 547 | <tr> |
|---|
| 548 | <th>Name</th> |
|---|
| 549 | <th>Type</th> |
|---|
| 550 | </tr> |
|---|
| 551 | <tr> |
|---|
| 552 | <td>Software A</td> |
|---|
| 553 | <td>Feature extraction</td> |
|---|
| 554 | </tr> |
|---|
| 555 | </table> |
|---|
| 556 | <p> |
|---|
| 557 | </li> |
|---|
| 558 | |
|---|
| 559 | <li> |
|---|
| 560 | Create annotation types: |
|---|
| 561 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 562 | <tr> |
|---|
| 563 | <th>Name</th> |
|---|
| 564 | <th>Type</th> |
|---|
| 565 | <th>Unit</th> |
|---|
| 566 | <th>Interface</th> |
|---|
| 567 | <th>Values</th> |
|---|
| 568 | <th>Item types</th> |
|---|
| 569 | </tr> |
|---|
| 570 | <tr> |
|---|
| 571 | <td>Drug resistance</td> |
|---|
| 572 | <td>String</td> |
|---|
| 573 | <td>-</td> |
|---|
| 574 | <td>radiobuttons</td> |
|---|
| 575 | <td>high, medium, low</td> |
|---|
| 576 | <td>Biosource</td> |
|---|
| 577 | </tr> |
|---|
| 578 | <tr> |
|---|
| 579 | <td>Time</td> |
|---|
| 580 | <td>Integer</td> |
|---|
| 581 | <td>Hour</td> |
|---|
| 582 | <td>text box</td> |
|---|
| 583 | <td>-</td> |
|---|
| 584 | <td>Sample</td> |
|---|
| 585 | </tr> |
|---|
| 586 | <tr> |
|---|
| 587 | <td>Dye swap</td> |
|---|
| 588 | <td>Boolean</td> |
|---|
| 589 | <td>-</td> |
|---|
| 590 | <td>-</td> |
|---|
| 591 | <td>-</td> |
|---|
| 592 | <td>Raw bioassay</td> |
|---|
| 593 | </tr> |
|---|
| 594 | </table> |
|---|
| 595 | <p> |
|---|
| 596 | |
|---|
| 597 | <li> |
|---|
| 598 | Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as |
|---|
| 599 | optional are not used in the test procedure, but may be useful to weed |
|---|
| 600 | out import problems, since they allow importing all info from the raw |
|---|
| 601 | data files. You may either enter the regular expressions as specified or |
|---|
| 602 | use the "Test with file" feature. |
|---|
| 603 | |
|---|
| 604 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 605 | <tr> |
|---|
| 606 | <th>Name</th> |
|---|
| 607 | <th>Plugin</th> |
|---|
| 608 | <th>Configuration values</th> |
|---|
| 609 | </tr> |
|---|
| 610 | |
|---|
| 611 | <tr class="oddrow"> |
|---|
| 612 | <td>Plates for project A</td> |
|---|
| 613 | <td>Plate importer</td> |
|---|
| 614 | <td> |
|---|
| 615 | |
|---|
| 616 | <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code> |
|---|
| 617 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 618 | <tr> |
|---|
| 619 | <td><i>Data header</i></td> |
|---|
| 620 | <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td> |
|---|
| 621 | </tr> |
|---|
| 622 | <tr> |
|---|
| 623 | <td><i>Data splitter</i></td> |
|---|
| 624 | <td>\t</td> |
|---|
| 625 | </tr> |
|---|
| 626 | <tr> |
|---|
| 627 | <td><i>Min data columns</i></td> |
|---|
| 628 | <td>5</td> |
|---|
| 629 | </tr> |
|---|
| 630 | <tr> |
|---|
| 631 | <td><i>Plate number/name</i></td> |
|---|
| 632 | <td>\384_number\</td> |
|---|
| 633 | </tr> |
|---|
| 634 | <tr> |
|---|
| 635 | <td><i>Row</i></td> |
|---|
| 636 | <td>\384_row\</td> |
|---|
| 637 | </tr> |
|---|
| 638 | <tr> |
|---|
| 639 | <td><i>Column</i></td> |
|---|
| 640 | <td>\384_column\</td> |
|---|
| 641 | </tr> |
|---|
| 642 | <tr> |
|---|
| 643 | <td><i>Reporter ID</i></td> |
|---|
| 644 | <td>\oligo_id\</td> |
|---|
| 645 | </tr> |
|---|
| 646 | </table> |
|---|
| 647 | |
|---|
| 648 | </td> |
|---|
| 649 | </tr> |
|---|
| 650 | |
|---|
| 651 | <tr class="evenrow"> |
|---|
| 652 | <td>GenePix feature importer<br>(optional)</td> |
|---|
| 653 | <td>Reporter map importer</td> |
|---|
| 654 | <td> |
|---|
| 655 | |
|---|
| 656 | <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code> |
|---|
| 657 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 658 | <tr> |
|---|
| 659 | <td><i>Data header</i></td> |
|---|
| 660 | <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td> |
|---|
| 661 | </tr> |
|---|
| 662 | <tr> |
|---|
| 663 | <td><i>Data splitter</i></td> |
|---|
| 664 | <td>\t</td> |
|---|
| 665 | </tr> |
|---|
| 666 | <tr> |
|---|
| 667 | <td><i>Min data columns</i></td> |
|---|
| 668 | <td>48</td> |
|---|
| 669 | </tr> |
|---|
| 670 | <tr> |
|---|
| 671 | <td><i>Max data columns</i></td> |
|---|
| 672 | <td>48</td> |
|---|
| 673 | </tr> |
|---|
| 674 | <tr> |
|---|
| 675 | <td><i>Reporter ID</i></td> |
|---|
| 676 | <td>\ID\</td> |
|---|
| 677 | </tr> |
|---|
| 678 | <tr> |
|---|
| 679 | <td><i>Block</i></td> |
|---|
| 680 | <td>\Block\</td> |
|---|
| 681 | </tr> |
|---|
| 682 | <tr> |
|---|
| 683 | <td><i>Column</i></td> |
|---|
| 684 | <td>\Column\</td> |
|---|
| 685 | </tr> |
|---|
| 686 | <tr> |
|---|
| 687 | <td><i>Row</i></td> |
|---|
| 688 | <td>\Row\</td> |
|---|
| 689 | </tr> |
|---|
| 690 | </table> |
|---|
| 691 | |
|---|
| 692 | </td> |
|---|
| 693 | </tr> |
|---|
| 694 | |
|---|
| 695 | <tr class="oddrow"> |
|---|
| 696 | <td>Raw data for project A</td> |
|---|
| 697 | <td>Raw data importer</td> |
|---|
| 698 | <td> |
|---|
| 699 | |
|---|
| 700 | <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code> |
|---|
| 701 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 702 | <tr> |
|---|
| 703 | <td><i>Raw data type</i></td> |
|---|
| 704 | <td>Genepix</td> |
|---|
| 705 | </tr> |
|---|
| 706 | <tr> |
|---|
| 707 | <td><i>Header</i></td> |
|---|
| 708 | <td>"(.+)=(.*)"</td> |
|---|
| 709 | </tr> |
|---|
| 710 | <tr> |
|---|
| 711 | <td><i>Data header</i></td> |
|---|
| 712 | <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(532\/635\)".*</td> |
|---|
| 713 | </tr> |
|---|
| 714 | <tr> |
|---|
| 715 | <td><i>Data splitter</i></td> |
|---|
| 716 | <td>\t</td> |
|---|
| 717 | </tr> |
|---|
| 718 | <tr> |
|---|
| 719 | <td><i>Min data columns</i></td> |
|---|
| 720 | <td>48</td> |
|---|
| 721 | </tr> |
|---|
| 722 | <tr> |
|---|
| 723 | <td><i>Max data columns</i></td> |
|---|
| 724 | <td>48</td> |
|---|
| 725 | </tr> |
|---|
| 726 | |
|---|
| 727 | <tr> |
|---|
| 728 | <td><i>Block</i></td> |
|---|
| 729 | <td>\Block\</td> |
|---|
| 730 | </tr> |
|---|
| 731 | <tr> |
|---|
| 732 | <td><i>Column</i></td> |
|---|
| 733 | <td>\Column\</td> |
|---|
| 734 | </tr> |
|---|
| 735 | <tr> |
|---|
| 736 | <td><i>Row</i></td> |
|---|
| 737 | <td>\Row\</td> |
|---|
| 738 | </tr> |
|---|
| 739 | <tr> |
|---|
| 740 | <td><i>X</i></td> |
|---|
| 741 | <td>\X\</td> |
|---|
| 742 | </tr> |
|---|
| 743 | <tr> |
|---|
| 744 | <td><i>Y</i></td> |
|---|
| 745 | <td>\Y\</td> |
|---|
| 746 | </tr> |
|---|
| 747 | <tr> |
|---|
| 748 | <td><i>Reporter ID</i></td> |
|---|
| 749 | <td>\ID\</td> |
|---|
| 750 | </tr> |
|---|
| 751 | <tr> |
|---|
| 752 | <td><i>Spot diameter</i></td> |
|---|
| 753 | <td>\Dia.\</td> |
|---|
| 754 | </tr> |
|---|
| 755 | <tr> |
|---|
| 756 | <td><i>Channel 1 foreground median</i></td> |
|---|
| 757 | <td>\F635 Median\</td> |
|---|
| 758 | </tr> |
|---|
| 759 | <tr> |
|---|
| 760 | <td><i>Channel 1 foreground mean</i></td> |
|---|
| 761 | <td>\F635 Mean\</td> |
|---|
| 762 | </tr> |
|---|
| 763 | <tr> |
|---|
| 764 | <td><i>Channel 1 foreground standard deviation</i></td> |
|---|
| 765 | <td>\F635 SD\</td> |
|---|
| 766 | </tr> |
|---|
| 767 | <tr> |
|---|
| 768 | <td><i>Channel 1 background median</i></td> |
|---|
| 769 | <td>\B635 Median\</td> |
|---|
| 770 | </tr> |
|---|
| 771 | <tr> |
|---|
| 772 | <td><i>Channel 1 background mean</i></td> |
|---|
| 773 | <td>\B635 Mean\</td> |
|---|
| 774 | </tr> |
|---|
| 775 | <tr> |
|---|
| 776 | <td><i>Channel 1 background standard deviation</i></td> |
|---|
| 777 | <td>\B635 SD\</td> |
|---|
| 778 | </tr> |
|---|
| 779 | <tr> |
|---|
| 780 | <td><i>Percent pixels within 1 standard deviation</i></td> |
|---|
| 781 | <td>\% > B635+1SD\</td> |
|---|
| 782 | </tr> |
|---|
| 783 | <tr> |
|---|
| 784 | <td><i>Percent pixels within 2 standard deviations</i></td> |
|---|
| 785 | <td>\% > B635+2SD\</td> |
|---|
| 786 | </tr> |
|---|
| 787 | <tr> |
|---|
| 788 | <td><i>Percent saturated pixels</i></td> |
|---|
| 789 | <td>\F635 % Sat.\</td> |
|---|
| 790 | </tr> |
|---|
| 791 | <tr> |
|---|
| 792 | <td><i>Channel 2 foreground median</i></td> |
|---|
| 793 | <td>\F532 Median\</td> |
|---|
| 794 | </tr> |
|---|
| 795 | <tr> |
|---|
| 796 | <td><i>Channel 2 foreground mean</i></td> |
|---|
| 797 | <td>\F532 Mean\</td> |
|---|
| 798 | </tr> |
|---|
| 799 | <tr> |
|---|
| 800 | <td><i>Channel 2 foreground standard deviation</i></td> |
|---|
| 801 | <td>\F532 SD\</td> |
|---|
| 802 | </tr> |
|---|
| 803 | <tr> |
|---|
| 804 | <td><i>Channel 2 background median</i></td> |
|---|
| 805 | <td>\B532 Median\</td> |
|---|
| 806 | </tr> |
|---|
| 807 | <tr> |
|---|
| 808 | <td><i>Channel 2 background mean</i></td> |
|---|
| 809 | <td>\B532 Mean\</td> |
|---|
| 810 | </tr> |
|---|
| 811 | <tr> |
|---|
| 812 | <td><i>Channel 2 background standard deviation</i></td> |
|---|
| 813 | <td>\B532 SD\</td> |
|---|
| 814 | </tr> |
|---|
| 815 | <tr> |
|---|
| 816 | <td><i>Percent pixels within 1 standard deviation</i></td> |
|---|
| 817 | <td>\% > B532+1SD\</td> |
|---|
| 818 | </tr> |
|---|
| 819 | <tr> |
|---|
| 820 | <td><i>Percent pixels within 2 standard deviations</i></td> |
|---|
| 821 | <td>\% > B532+2SD\</td> |
|---|
| 822 | </tr> |
|---|
| 823 | <tr> |
|---|
| 824 | <td><i>Percent saturated pixels</i></td> |
|---|
| 825 | <td>\F532 % Sat.\</td> |
|---|
| 826 | </tr> |
|---|
| 827 | <tr> |
|---|
| 828 | <td><i>Foreground pixels</i></td> |
|---|
| 829 | <td>\F Pixels\</td> |
|---|
| 830 | </tr> |
|---|
| 831 | <tr> |
|---|
| 832 | <td><i>Background pixels</i></td> |
|---|
| 833 | <td>\B Pixels\</td> |
|---|
| 834 | </tr> |
|---|
| 835 | <tr> |
|---|
| 836 | <td><i>Flags</i></td> |
|---|
| 837 | <td>\Flags\</td> |
|---|
| 838 | </tr> |
|---|
| 839 | </table> |
|---|
| 840 | |
|---|
| 841 | </td> |
|---|
| 842 | </tr> |
|---|
| 843 | |
|---|
| 844 | <tr class="evenrow"> |
|---|
| 845 | <td>Raw data for project A (dye-swap)</td> |
|---|
| 846 | <td>Raw data importer</td> |
|---|
| 847 | <td> |
|---|
| 848 | |
|---|
| 849 | <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code> |
|---|
| 850 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 851 | <tr> |
|---|
| 852 | <td><i>Raw data type</i></td> |
|---|
| 853 | <td>Genepix</td> |
|---|
| 854 | </tr> |
|---|
| 855 | <tr> |
|---|
| 856 | <td><i>Header</i></td> |
|---|
| 857 | <td>"(.+)=(.*)"</td> |
|---|
| 858 | </tr> |
|---|
| 859 | <tr> |
|---|
| 860 | <td><i>Data header</i></td> |
|---|
| 861 | <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(635\/532\)".*</td> |
|---|
| 862 | </tr> |
|---|
| 863 | <tr> |
|---|
| 864 | <td><i>Data splitter</i></td> |
|---|
| 865 | <td>\t</td> |
|---|
| 866 | </tr> |
|---|
| 867 | <tr> |
|---|
| 868 | <td><i>Min data columns</i></td> |
|---|
| 869 | <td>48</td> |
|---|
| 870 | </tr> |
|---|
| 871 | <tr> |
|---|
| 872 | <td><i>Max data columns</i></td> |
|---|
| 873 | <td>48</td> |
|---|
| 874 | </tr> |
|---|
| 875 | |
|---|
| 876 | <tr> |
|---|
| 877 | <td><i>Block</i></td> |
|---|
| 878 | <td>\Block\</td> |
|---|
| 879 | </tr> |
|---|
| 880 | <tr> |
|---|
| 881 | <td><i>Column</i></td> |
|---|
| 882 | <td>\Column\</td> |
|---|
| 883 | </tr> |
|---|
| 884 | <tr> |
|---|
| 885 | <td><i>Row</i></td> |
|---|
| 886 | <td>\Row\</td> |
|---|
| 887 | </tr> |
|---|
| 888 | <tr> |
|---|
| 889 | <td><i>X</i></td> |
|---|
| 890 | <td>\X\</td> |
|---|
| 891 | </tr> |
|---|
| 892 | <tr> |
|---|
| 893 | <td><i>Y</i></td> |
|---|
| 894 | <td>\Y\</td> |
|---|
| 895 | </tr> |
|---|
| 896 | <tr> |
|---|
| 897 | <td><i>Reporter ID</i></td> |
|---|
| 898 | <td>\ID\</td> |
|---|
| 899 | </tr> |
|---|
| 900 | <tr> |
|---|
| 901 | <td><i>Spot diameter</i></td> |
|---|
| 902 | <td>\Dia.\</td> |
|---|
| 903 | </tr> |
|---|
| 904 | <tr> |
|---|
| 905 | <td><i>Channel 1 foreground median</i></td> |
|---|
| 906 | <td>\F532 Median\</td> |
|---|
| 907 | </tr> |
|---|
| 908 | <tr> |
|---|
| 909 | <td><i>Channel 1 foreground mean</i></td> |
|---|
| 910 | <td>\F532 Mean\</td> |
|---|
| 911 | </tr> |
|---|
| 912 | <tr> |
|---|
| 913 | <td><i>Channel 1 foreground standard deviation</i></td> |
|---|
| 914 | <td>\F532 SD\</td> |
|---|
| 915 | </tr> |
|---|
| 916 | <tr> |
|---|
| 917 | <td><i>Channel 1 background median</i></td> |
|---|
| 918 | <td>\B532 Median\</td> |
|---|
| 919 | </tr> |
|---|
| 920 | <tr> |
|---|
| 921 | <td><i>Channel 1 background mean</i></td> |
|---|
| 922 | <td>\B532 Mean\</td> |
|---|
| 923 | </tr> |
|---|
| 924 | <tr> |
|---|
| 925 | <td><i>Channel 1 background standard deviation</i></td> |
|---|
| 926 | <td>\B532 SD\</td> |
|---|
| 927 | </tr> |
|---|
| 928 | <tr> |
|---|
| 929 | <td><i>Percent pixels within 1 standard deviation</i></td> |
|---|
| 930 | <td>\% > B532+1SD\</td> |
|---|
| 931 | </tr> |
|---|
| 932 | <tr> |
|---|
| 933 | <td><i>Percent pixels within 2 standard deviations</i></td> |
|---|
| 934 | <td>\% > B532+2SD\</td> |
|---|
| 935 | </tr> |
|---|
| 936 | <tr> |
|---|
| 937 | <td><i>Percent saturated pixels</i></td> |
|---|
| 938 | <td>\F532 % Sat.\</td> |
|---|
| 939 | </tr> |
|---|
| 940 | <tr> |
|---|
| 941 | <td><i>Channel 2 foreground median</i></td> |
|---|
| 942 | <td>\F635 Median\</td> |
|---|
| 943 | </tr> |
|---|
| 944 | <tr> |
|---|
| 945 | <td><i>Channel 2 foreground mean</i></td> |
|---|
| 946 | <td>\F635 Mean\</td> |
|---|
| 947 | </tr> |
|---|
| 948 | <tr> |
|---|
| 949 | <td><i>Channel 2 foreground standard deviation</i></td> |
|---|
| 950 | <td>\F635 SD\</td> |
|---|
| 951 | </tr> |
|---|
| 952 | <tr> |
|---|
| 953 | <td><i>Channel 2 background median</i></td> |
|---|
| 954 | <td>\B635 Median\</td> |
|---|
| 955 | </tr> |
|---|
| 956 | <tr> |
|---|
| 957 | <td><i>Channel 2 background mean</i></td> |
|---|
| 958 | <td>\B635 Mean\</td> |
|---|
| 959 | </tr> |
|---|
| 960 | <tr> |
|---|
| 961 | <td><i>Channel 2 background standard deviation</i></td> |
|---|
| 962 | <td>\B635 SD\</td> |
|---|
| 963 | </tr> |
|---|
| 964 | <tr> |
|---|
| 965 | <td><i>Percent pixels within 1 standard deviation</i></td> |
|---|
| 966 | <td>\% > B635+1SD\</td> |
|---|
| 967 | </tr> |
|---|
| 968 | <tr> |
|---|
| 969 | <td><i>Percent pixels within 2 standard deviations</i></td> |
|---|
| 970 | <td>\% > B635+2SD\</td> |
|---|
| 971 | </tr> |
|---|
| 972 | <tr> |
|---|
| 973 | <td><i>Percent saturated pixels</i></td> |
|---|
| 974 | <td>\F635 % Sat.\</td> |
|---|
| 975 | </tr> |
|---|
| 976 | <tr> |
|---|
| 977 | <td><i>Foreground pixels</i></td> |
|---|
| 978 | <td>\F Pixels\</td> |
|---|
| 979 | </tr> |
|---|
| 980 | <tr> |
|---|
| 981 | <td><i>Background pixels</i></td> |
|---|
| 982 | <td>\B Pixels\</td> |
|---|
| 983 | </tr> |
|---|
| 984 | <tr> |
|---|
| 985 | <td><i>Flags</i></td> |
|---|
| 986 | <td>\Flags\</td> |
|---|
| 987 | </tr> |
|---|
| 988 | </table> |
|---|
| 989 | |
|---|
| 990 | </td> |
|---|
| 991 | </tr> |
|---|
| 992 | </table> |
|---|
| 993 | <p> |
|---|
| 994 | </li> |
|---|
| 995 | |
|---|
| 996 | <li> |
|---|
| 997 | Annotate the file formats: |
|---|
| 998 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 999 | <tr> |
|---|
| 1000 | <th>File format</th> |
|---|
| 1001 | <th>Annotation</th> |
|---|
| 1002 | <th>Value</th> |
|---|
| 1003 | </tr> |
|---|
| 1004 | <tr> |
|---|
| 1005 | <td>Raw data for project A</td> |
|---|
| 1006 | <td>Dye swap</td> |
|---|
| 1007 | <td>false</td> |
|---|
| 1008 | </tr> |
|---|
| 1009 | <tr> |
|---|
| 1010 | <td>Raw data for project A (dye swap)</td> |
|---|
| 1011 | <td>Dye swap</td> |
|---|
| 1012 | <td>true</td> |
|---|
| 1013 | </tr> |
|---|
| 1014 | </table> |
|---|
| 1015 | This will make the raw data importer automatically annotate the |
|---|
| 1016 | raw bioassays with the specified annotations. |
|---|
| 1017 | <p> |
|---|
| 1018 | </li> |
|---|
| 1019 | |
|---|
| 1020 | <li> |
|---|
| 1021 | Create plate type: |
|---|
| 1022 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1023 | <tr> |
|---|
| 1024 | <th>Name</th> |
|---|
| 1025 | <th>Geometry</th> |
|---|
| 1026 | </tr> |
|---|
| 1027 | <tr> |
|---|
| 1028 | <td>Plate type A</td> |
|---|
| 1029 | <td>384-well (16 x 24)</td> |
|---|
| 1030 | </tr> |
|---|
| 1031 | </table> |
|---|
| 1032 | <p> |
|---|
| 1033 | </li> |
|---|
| 1034 | |
|---|
| 1035 | <li> |
|---|
| 1036 | Import plates: |
|---|
| 1037 | <ol> |
|---|
| 1038 | <li>Go to the <code>Array LIMS -> Plates</code> page.</li> |
|---|
| 1039 | <li>Click on the <code>Import</code> button.</li> |
|---|
| 1040 | <li>Choose <code>auto-detect</code> and select |
|---|
| 1041 | the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li> |
|---|
| 1042 | <li>The <code>Plates for project A</code> format should be |
|---|
| 1043 | found.</li> |
|---|
| 1044 | <li>Specify the following parameters: |
|---|
| 1045 | |
|---|
| 1046 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 1047 | <tr> |
|---|
| 1048 | <td><i>Plate type</i></td> |
|---|
| 1049 | <td>Plate type A</td> |
|---|
| 1050 | </tr> |
|---|
| 1051 | <tr> |
|---|
| 1052 | <td><i>Plate name prefix</i></td> |
|---|
| 1053 | <td>Plate A</td> |
|---|
| 1054 | </tr> |
|---|
| 1055 | <tr> |
|---|
| 1056 | <td><i>Plate name padding</i></td> |
|---|
| 1057 | <td>4</td> |
|---|
| 1058 | </tr> |
|---|
| 1059 | </table> |
|---|
| 1060 | </li> |
|---|
| 1061 | <li>Continue and wait for the import to finish. It should create 96 plates.</li> |
|---|
| 1062 | </ol> |
|---|
| 1063 | <p> |
|---|
| 1064 | </li> |
|---|
| 1065 | |
|---|
| 1066 | <li> |
|---|
| 1067 | Create array designs and upload data files to them: |
|---|
| 1068 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1069 | <tr> |
|---|
| 1070 | <th>Name</th> |
|---|
| 1071 | <th>Platform</th> |
|---|
| 1072 | <th>File(s)</th> |
|---|
| 1073 | </tr> |
|---|
| 1074 | <tr> |
|---|
| 1075 | <td>Array design A</td> |
|---|
| 1076 | <td>Generic</td> |
|---|
| 1077 | <td><i>Print map</i>: printmap.mouse.v4.37k.tam</td> |
|---|
| 1078 | </tr> |
|---|
| 1079 | <tr> |
|---|
| 1080 | <td>Affymetrix A</td> |
|---|
| 1081 | <td>Affymetrix</td> |
|---|
| 1082 | <td><i>CDF file</i>: MG_U74Av2.cdf.bz2</td> |
|---|
| 1083 | </tr> |
|---|
| 1084 | </table> |
|---|
| 1085 | <p> |
|---|
| 1086 | Or |
|---|
| 1087 | <p> |
|---|
| 1088 | Import array designs with the ArrayDesignImporter plug-in. |
|---|
| 1089 | <ol> |
|---|
| 1090 | <li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li> |
|---|
| 1091 | <li>Click on the <code>Import</code> button on the array design list page.</li> |
|---|
| 1092 | <li>Choose ArrayDesignImporter in the plug-in drop-down list.</li> |
|---|
| 1093 | <li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set |
|---|
| 1094 | the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code> |
|---|
| 1095 | tab.</li> |
|---|
| 1096 | <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li> |
|---|
| 1097 | </ol> |
|---|
| 1098 | <p> |
|---|
| 1099 | </li> |
|---|
| 1100 | |
|---|
| 1101 | <li> |
|---|
| 1102 | Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting |
|---|
| 1103 | with <code>Plate A</code>) and sort them in the correct order (as indicated by their names). |
|---|
| 1104 | <p> |
|---|
| 1105 | </li> |
|---|
| 1106 | |
|---|
| 1107 | <li> |
|---|
| 1108 | Import features: |
|---|
| 1109 | <ol> |
|---|
| 1110 | <li>Click on the <code>Import</code> button when viewing properties for the array design.</li> |
|---|
| 1111 | <li>Choose <code>auto-detect</code> and upload the file |
|---|
| 1112 | <code>printmap.mouse.v4.37k.tam</code>.</li> |
|---|
| 1113 | <li>The <code>Print map importer</code> plug-in should be |
|---|
| 1114 | found.</li> |
|---|
| 1115 | <li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li> |
|---|
| 1116 | </ol> |
|---|
| 1117 | <p> |
|---|
| 1118 | </li> |
|---|
| 1119 | |
|---|
| 1120 | <li> |
|---|
| 1121 | Set project defaults. Go to the projects page and edit the |
|---|
| 1122 | <code>Project A</code> project. On the <code>Defaults</code> |
|---|
| 1123 | tab, set the following defaults: |
|---|
| 1124 | |
|---|
| 1125 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1126 | <tr> |
|---|
| 1127 | <th>Setting</th> |
|---|
| 1128 | <th>Value</th> |
|---|
| 1129 | </tr> |
|---|
| 1130 | <tr> |
|---|
| 1131 | <td>Platform / raw data type</td> |
|---|
| 1132 | <td>Generic / Genepix</td> |
|---|
| 1133 | </tr> |
|---|
| 1134 | <tr> |
|---|
| 1135 | <td>Software</td> |
|---|
| 1136 | <td>Software A</td> |
|---|
| 1137 | </tr> |
|---|
| 1138 | <tr> |
|---|
| 1139 | <td>Array design</td> |
|---|
| 1140 | <td>Array design A</td> |
|---|
| 1141 | </tr> |
|---|
| 1142 | <tr> |
|---|
| 1143 | <td>Hybridization station</td> |
|---|
| 1144 | <td>Hybridization station A</td> |
|---|
| 1145 | </tr> |
|---|
| 1146 | <tr> |
|---|
| 1147 | <td>Scanner</td> |
|---|
| 1148 | <td>Scanner A</td> |
|---|
| 1149 | </tr> |
|---|
| 1150 | <tr> |
|---|
| 1151 | <td>Print robot</td> |
|---|
| 1152 | <td>Print robot A</td> |
|---|
| 1153 | </tr> |
|---|
| 1154 | <tr> |
|---|
| 1155 | <td>Scanning protocol</td> |
|---|
| 1156 | <td>Scanning A</td> |
|---|
| 1157 | </tr> |
|---|
| 1158 | <tr> |
|---|
| 1159 | <td>Sampling protocol</td> |
|---|
| 1160 | <td>Sampling A</td> |
|---|
| 1161 | </tr> |
|---|
| 1162 | <tr> |
|---|
| 1163 | <td>Extraction protocol</td> |
|---|
| 1164 | <td>Extraction A</td> |
|---|
| 1165 | </tr> |
|---|
| 1166 | <tr> |
|---|
| 1167 | <td>Labeling protocol</td> |
|---|
| 1168 | <td>Labeling A</td> |
|---|
| 1169 | </tr> |
|---|
| 1170 | <tr> |
|---|
| 1171 | <td>Hybridization protocol</td> |
|---|
| 1172 | <td>Hybridization A</td> |
|---|
| 1173 | </tr> |
|---|
| 1174 | <tr> |
|---|
| 1175 | <td>Feat. extraction protocol</td> |
|---|
| 1176 | <td>Feature extraction A</td> |
|---|
| 1177 | </tr> |
|---|
| 1178 | <tr> |
|---|
| 1179 | <td>Printing protocol</td> |
|---|
| 1180 | <td>Printing A</td> |
|---|
| 1181 | </tr> |
|---|
| 1182 | </table> |
|---|
| 1183 | |
|---|
| 1184 | <p> |
|---|
| 1185 | </li> |
|---|
| 1186 | |
|---|
| 1187 | <li> |
|---|
| 1188 | Create array batches: |
|---|
| 1189 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1190 | <tr> |
|---|
| 1191 | <th>Name</th> |
|---|
| 1192 | <th>Array design</th> |
|---|
| 1193 | <th>Print robot</th> |
|---|
| 1194 | <th>Protocol</th> |
|---|
| 1195 | </tr> |
|---|
| 1196 | <tr> |
|---|
| 1197 | <td>Array batch A</td> |
|---|
| 1198 | <td>Array design A</td> |
|---|
| 1199 | <td>Robot A</td> |
|---|
| 1200 | <td>Printing A</td> |
|---|
| 1201 | </tr> |
|---|
| 1202 | <tr> |
|---|
| 1203 | <td>Affymetrix batch A</td> |
|---|
| 1204 | <td>Affymetrix A</td> |
|---|
| 1205 | <td></td> |
|---|
| 1206 | <td></td> |
|---|
| 1207 | </tr> |
|---|
| 1208 | </table> |
|---|
| 1209 | <p> |
|---|
| 1210 | Or |
|---|
| 1211 | <p> |
|---|
| 1212 | Import array batches with the ArrayBatchImporter plug-in. |
|---|
| 1213 | <ol> |
|---|
| 1214 | <li>Click on the <code>Import</code> button on the array batch list page.</li> |
|---|
| 1215 | <li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li> |
|---|
| 1216 | <li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set the parsing parameters |
|---|
| 1217 | with help of the <code>Auto generate</code> button on the <code>Column mapping</code> |
|---|
| 1218 | tab.</li> |
|---|
| 1219 | <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li> |
|---|
| 1220 | </ol> |
|---|
| 1221 | <p> |
|---|
| 1222 | </li> |
|---|
| 1223 | |
|---|
| 1224 | <li> |
|---|
| 1225 | Create array slides with the <code>Create slides</code> |
|---|
| 1226 | wizard. |
|---|
| 1227 | |
|---|
| 1228 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1229 | <tr> |
|---|
| 1230 | <th>Name</th> |
|---|
| 1231 | <th>Array batch</th> |
|---|
| 1232 | <th>Quantity</th> |
|---|
| 1233 | </tr> |
|---|
| 1234 | <tr> |
|---|
| 1235 | <td>Array slide A.</td> |
|---|
| 1236 | <td>Array batch A</td> |
|---|
| 1237 | <td>4</td> |
|---|
| 1238 | </tr> |
|---|
| 1239 | <tr> |
|---|
| 1240 | <td>Affymetrix slide A.</td> |
|---|
| 1241 | <td>Affymetrix batch A</td> |
|---|
| 1242 | <td>3</td> |
|---|
| 1243 | </tr> |
|---|
| 1244 | </table> |
|---|
| 1245 | <p> |
|---|
| 1246 | Or |
|---|
| 1247 | <p> |
|---|
| 1248 | Import array slides with the ArraySlideImporter plug-in. |
|---|
| 1249 | <ol> |
|---|
| 1250 | <li>Click on the <code>Import</code> button on the array slide list page.</li> |
|---|
| 1251 | <li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li> |
|---|
| 1252 | <li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set the parsing parameters |
|---|
| 1253 | with help of the <code>Auto generate</code> button on the <code>Column mapping</code> |
|---|
| 1254 | tab.</li> |
|---|
| 1255 | <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li> |
|---|
| 1256 | </ol> |
|---|
| 1257 | <p> |
|---|
| 1258 | </li> |
|---|
| 1259 | </ol> |
|---|
| 1260 | |
|---|
| 1261 | <a name="user"></a> |
|---|
| 1262 | <h2>5. User tests</h2> |
|---|
| 1263 | <p> |
|---|
| 1264 | The user is a typical worker in the project. The user does the actual experimentation in the |
|---|
| 1265 | lab, which includes collecting samples, doing extraction, labeling and hybridizations. |
|---|
| 1266 | The user also scans and analyses the raw data resulting from the images. Inserting items can be |
|---|
| 1267 | done in two different ways, . |
|---|
| 1268 | </p> |
|---|
| 1269 | <h3>First step</h3> |
|---|
| 1270 | |
|---|
| 1271 | <ol> |
|---|
| 1272 | <li>Activate the <code>Project A</code> project. |
|---|
| 1273 | <p> |
|---|
| 1274 | <li> |
|---|
| 1275 | Create a bioplate: |
|---|
| 1276 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1277 | <tr> |
|---|
| 1278 | <th>Name</th> |
|---|
| 1279 | <th>Plate geometry</th> |
|---|
| 1280 | </tr> |
|---|
| 1281 | <tr> |
|---|
| 1282 | <td>Bioplate A</td> |
|---|
| 1283 | <td>96-well (8 x 12)</td> |
|---|
| 1284 | </tr> |
|---|
| 1285 | </table> |
|---|
| 1286 | <p> |
|---|
| 1287 | <li>Continue with the second step, which can be done with batch importers or |
|---|
| 1288 | manually. |
|---|
| 1289 | |
|---|
| 1290 | </ol> |
|---|
| 1291 | |
|---|
| 1292 | |
|---|
| 1293 | <h3>Second step (using batch importers)</h3> |
|---|
| 1294 | |
|---|
| 1295 | <ol> |
|---|
| 1296 | <li>Click on the <code>Import</code> button on the list page.</li> |
|---|
| 1297 | <li>Select <itemtype>Importer in the plug-in drop-down list and click <code>Next</code></li> |
|---|
| 1298 | <li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters |
|---|
| 1299 | by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab. |
|---|
| 1300 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1301 | <tr> |
|---|
| 1302 | <th>Itemtype</th> |
|---|
| 1303 | <th>File</th> |
|---|
| 1304 | </tr> |
|---|
| 1305 | <tr> |
|---|
| 1306 | <td>Biosource</td> |
|---|
| 1307 | <td>biosource_out.txt</td> |
|---|
| 1308 | </tr> |
|---|
| 1309 | <tr> |
|---|
| 1310 | <td>Samples</td> |
|---|
| 1311 | <td>sample_out.txt</td> |
|---|
| 1312 | </tr> |
|---|
| 1313 | <tr> |
|---|
| 1314 | <td>Extracts</td> |
|---|
| 1315 | <td>extract_out.txt</td> |
|---|
| 1316 | </tr> |
|---|
| 1317 | <tr> |
|---|
| 1318 | <td>Labeled extracts</td> |
|---|
| 1319 | <td>labeledextract_out.txt</td> |
|---|
| 1320 | </tr> |
|---|
| 1321 | <tr> |
|---|
| 1322 | <td>Hybridizations</td> |
|---|
| 1323 | <td>hybridization_out.txt</td> |
|---|
| 1324 | </tr> |
|---|
| 1325 | <tr> |
|---|
| 1326 | <td>Scans</td> |
|---|
| 1327 | <td>scan_out.txt</td> |
|---|
| 1328 | </tr> |
|---|
| 1329 | <tr> |
|---|
| 1330 | <td>Raw bioassays</td> |
|---|
| 1331 | <td>rawbioassay_out.txt</td> |
|---|
| 1332 | </tr> |
|---|
| 1333 | </table> |
|---|
| 1334 | The files listed for biosource and samples also contains annotations |
|---|
| 1335 | for the items and these files should also be used with the annotation importer. |
|---|
| 1336 | The procedure is the same as for batch importers except that only <code>\Name\</code> |
|---|
| 1337 | is needed in the column mapping. The annotation column should be selected by default in |
|---|
| 1338 | the second wizzard-step. |
|---|
| 1339 | </li> |
|---|
| 1340 | <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li> |
|---|
| 1341 | <li>Continue with <a href="#step3">the third step</a>.</li> |
|---|
| 1342 | </ol> |
|---|
| 1343 | |
|---|
| 1344 | <h3>Second step (create items manually)</h3> |
|---|
| 1345 | <ol> |
|---|
| 1346 | <li> |
|---|
| 1347 | Create a biosource: |
|---|
| 1348 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1349 | <tr> |
|---|
| 1350 | <th>Name</th> |
|---|
| 1351 | <th>Annotations</th> |
|---|
| 1352 | </tr> |
|---|
| 1353 | <tr> |
|---|
| 1354 | <td>Biosource A</td> |
|---|
| 1355 | <td> |
|---|
| 1356 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 1357 | <tr> |
|---|
| 1358 | <td><i>Drug resistance:</i></td> |
|---|
| 1359 | <td>medium</td> |
|---|
| 1360 | </tr> |
|---|
| 1361 | </table> |
|---|
| 1362 | </td> |
|---|
| 1363 | </tr> |
|---|
| 1364 | </table> |
|---|
| 1365 | <p> |
|---|
| 1366 | </li> |
|---|
| 1367 | |
|---|
| 1368 | <li> |
|---|
| 1369 | Create samples: |
|---|
| 1370 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1371 | <tr> |
|---|
| 1372 | <th>Name</th> |
|---|
| 1373 | <th>Protocol</th> |
|---|
| 1374 | <th>Biosource</th> |
|---|
| 1375 | <th>Bioplate [well]</th> |
|---|
| 1376 | <th>Annotations</th> |
|---|
| 1377 | </tr> |
|---|
| 1378 | <tr> |
|---|
| 1379 | <td>Sample A.00h</td> |
|---|
| 1380 | <td>Sampling A</td> |
|---|
| 1381 | <td>Biosource A</td> |
|---|
| 1382 | <td>Bioplate A [0, 0]</td> |
|---|
| 1383 | <td> |
|---|
| 1384 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 1385 | <tr> |
|---|
| 1386 | <td><i>Time:</i></td> |
|---|
| 1387 | <td>0h</td> |
|---|
| 1388 | </tr> |
|---|
| 1389 | </table> |
|---|
| 1390 | </td> |
|---|
| 1391 | </tr> |
|---|
| 1392 | <tr> |
|---|
| 1393 | <td>Sample A.24h</td> |
|---|
| 1394 | <td>Sampling A</td> |
|---|
| 1395 | <td>Biosource A</td> |
|---|
| 1396 | <td>Bioplate A [0, 1]</td> |
|---|
| 1397 | <td> |
|---|
| 1398 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 1399 | <tr> |
|---|
| 1400 | <td><i>Time:</i></td> |
|---|
| 1401 | <td>24h</td> |
|---|
| 1402 | </tr> |
|---|
| 1403 | </table> |
|---|
| 1404 | </td> |
|---|
| 1405 | </tr> |
|---|
| 1406 | <tr> |
|---|
| 1407 | <td>Sample A.ref</td> |
|---|
| 1408 | <td>Sampling A</td> |
|---|
| 1409 | <td>-</td> |
|---|
| 1410 | <td>Bioplate A [0, 2]</td> |
|---|
| 1411 | <td>-</td> |
|---|
| 1412 | </tr> |
|---|
| 1413 | </table> |
|---|
| 1414 | <p> |
|---|
| 1415 | </li> |
|---|
| 1416 | |
|---|
| 1417 | <li> |
|---|
| 1418 | Create extracts: |
|---|
| 1419 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1420 | <tr> |
|---|
| 1421 | <th>Name</th> |
|---|
| 1422 | <th>Protocol</th> |
|---|
| 1423 | <th>Sample</th> |
|---|
| 1424 | <th>Bioplate [well]</th> |
|---|
| 1425 | </tr> |
|---|
| 1426 | <tr> |
|---|
| 1427 | <td>Extract A.00h</td> |
|---|
| 1428 | <td>Extraction A</td> |
|---|
| 1429 | <td>Sample A.00h</td> |
|---|
| 1430 | <td>Bioplate A [1, 0]</td> |
|---|
| 1431 | </tr> |
|---|
| 1432 | <tr> |
|---|
| 1433 | <td>Extract A.24h</td> |
|---|
| 1434 | <td>Extraction A</td> |
|---|
| 1435 | <td>Sample A.24h</td> |
|---|
| 1436 | <td>Bioplate A [1, 1]</td> |
|---|
| 1437 | </tr> |
|---|
| 1438 | <tr> |
|---|
| 1439 | <td>Extract A.ref</td> |
|---|
| 1440 | <td>Extraction A</td> |
|---|
| 1441 | <td>Sample A.ref</td> |
|---|
| 1442 | <td>Bioplate A [1, 2]</td> |
|---|
| 1443 | </tr> |
|---|
| 1444 | </table> |
|---|
| 1445 | <p> |
|---|
| 1446 | </li> |
|---|
| 1447 | |
|---|
| 1448 | <li> |
|---|
| 1449 | Create labeled extracts: |
|---|
| 1450 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1451 | <tr> |
|---|
| 1452 | <th>Name</th> |
|---|
| 1453 | <th>Label</th> |
|---|
| 1454 | <th>Protocol</th> |
|---|
| 1455 | <th>Extract</th> |
|---|
| 1456 | <th>Bioplate [well]</th> |
|---|
| 1457 | </tr> |
|---|
| 1458 | <tr> |
|---|
| 1459 | <td>Labeled extract A.00h</td> |
|---|
| 1460 | <td>cy3</td> |
|---|
| 1461 | <td>Labeling A</td> |
|---|
| 1462 | <td>Extract A.00h</td> |
|---|
| 1463 | <td>Bioplate A [2, 0]</td> |
|---|
| 1464 | </tr> |
|---|
| 1465 | <tr> |
|---|
| 1466 | <td>Labeled extract A.24h</td> |
|---|
| 1467 | <td>cy3</td> |
|---|
| 1468 | <td>Labeling A</td> |
|---|
| 1469 | <td>Extract A.24h</td> |
|---|
| 1470 | <td>Bioplate A [2, 1]</td> |
|---|
| 1471 | </tr> |
|---|
| 1472 | <tr> |
|---|
| 1473 | <td>Labeled extract A.ref</td> |
|---|
| 1474 | <td>cy5</td> |
|---|
| 1475 | <td>Labeling A</td> |
|---|
| 1476 | <td>Extract A.ref</td> |
|---|
| 1477 | <td>Bioplate A [2, 2]</td> |
|---|
| 1478 | </tr> |
|---|
| 1479 | <tr class="shaded"> |
|---|
| 1480 | <td>Labeled extract A.00h (dye-swap)</td> |
|---|
| 1481 | <td>cy5</td> |
|---|
| 1482 | <td>Labeling A</td> |
|---|
| 1483 | <td>Extract A.00h</td> |
|---|
| 1484 | <td>Bioplate A [3, 0]</td> |
|---|
| 1485 | </tr> |
|---|
| 1486 | <tr class="shaded"> |
|---|
| 1487 | <td>Labeled extract A.24h (dye-swap)</td> |
|---|
| 1488 | <td>cy5</td> |
|---|
| 1489 | <td>Labeling A</td> |
|---|
| 1490 | <td>Extract A.24h</td> |
|---|
| 1491 | <td>Bioplate A [3, 1]</td> |
|---|
| 1492 | </tr> |
|---|
| 1493 | <tr class="shaded"> |
|---|
| 1494 | <td>Labeled extract A.ref (dye-swap)</td> |
|---|
| 1495 | <td>cy3</td> |
|---|
| 1496 | <td>Labeling A</td> |
|---|
| 1497 | <td>Extract A.ref</td> |
|---|
| 1498 | <td>Bioplate A [3, 2]</td> |
|---|
| 1499 | </tr> |
|---|
| 1500 | </table> |
|---|
| 1501 | <p> |
|---|
| 1502 | </li> |
|---|
| 1503 | |
|---|
| 1504 | <li> |
|---|
| 1505 | Create hybridizations: |
|---|
| 1506 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1507 | <tr> |
|---|
| 1508 | <th>Name</th> |
|---|
| 1509 | <th>Protocol</th> |
|---|
| 1510 | <th>Hardware</th> |
|---|
| 1511 | <th>Array slide</th> |
|---|
| 1512 | <th>Labeled extracts</th> |
|---|
| 1513 | </tr> |
|---|
| 1514 | <tr> |
|---|
| 1515 | <td>Hybridization A.00h</td> |
|---|
| 1516 | <td>Hybridization A</td> |
|---|
| 1517 | <td>Hybridization station A</td> |
|---|
| 1518 | <td>Array slide A.1</td> |
|---|
| 1519 | <td>Labeled extract A.00h,<br>Labeled extract A.ref</td> |
|---|
| 1520 | </tr> |
|---|
| 1521 | <tr> |
|---|
| 1522 | <td>Hybridization A.24h</td> |
|---|
| 1523 | <td>Hybridization A</td> |
|---|
| 1524 | <td>Hybridization station A</td> |
|---|
| 1525 | <td>Array slide A.2</td> |
|---|
| 1526 | <td>Labeled extract A.24h,<br>Labeled extract A.ref</td> |
|---|
| 1527 | </tr> |
|---|
| 1528 | <tr class="shaded"> |
|---|
| 1529 | <td>Hybridization A.00h (dye-swap)</td> |
|---|
| 1530 | <td>Hybridization A</td> |
|---|
| 1531 | <td>Hybridization station A</td> |
|---|
| 1532 | <td>Array slide A.3</td> |
|---|
| 1533 | <td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td> |
|---|
| 1534 | </tr> |
|---|
| 1535 | <tr class="shaded"> |
|---|
| 1536 | <td>Hybridization A.24h (dye-swap)</td> |
|---|
| 1537 | <td>Hybridization A</td> |
|---|
| 1538 | <td>Hybridization station A</td> |
|---|
| 1539 | <td>Array slide A.4</td> |
|---|
| 1540 | <td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td> |
|---|
| 1541 | </tr> |
|---|
| 1542 | <tr> |
|---|
| 1543 | <td>Affymetrix hyb A.1</td> |
|---|
| 1544 | <td>Hybridization A</td> |
|---|
| 1545 | <td>Hybridization station A</td> |
|---|
| 1546 | <td>Affymetrix slide A.1</td> |
|---|
| 1547 | <td>Labeled extract A.00h</td> |
|---|
| 1548 | </tr> |
|---|
| 1549 | <tr> |
|---|
| 1550 | <td>Affymetrix hyb A.2</td> |
|---|
| 1551 | <td>Hybridization A</td> |
|---|
| 1552 | <td>Hybridization station A</td> |
|---|
| 1553 | <td>Affymetrix slide A.2</td> |
|---|
| 1554 | <td>Labeled extract A.24h</td> |
|---|
| 1555 | </tr> |
|---|
| 1556 | <tr> |
|---|
| 1557 | <td>Affymetrix hyb A.3</td> |
|---|
| 1558 | <td>Hybridization A</td> |
|---|
| 1559 | <td>Hybridization station A</td> |
|---|
| 1560 | <td>Affymetrix slide A.3</td> |
|---|
| 1561 | <td>Labeled extract A.ref</td> |
|---|
| 1562 | </tr> |
|---|
| 1563 | </table> |
|---|
| 1564 | <p> |
|---|
| 1565 | </li> |
|---|
| 1566 | |
|---|
| 1567 | <li> |
|---|
| 1568 | Create scans: |
|---|
| 1569 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1570 | <tr> |
|---|
| 1571 | <th>Name</th> |
|---|
| 1572 | <th>Hybridization</th> |
|---|
| 1573 | <th>Scanner</th> |
|---|
| 1574 | <th>Protocol</th> |
|---|
| 1575 | </tr> |
|---|
| 1576 | <tr> |
|---|
| 1577 | <td>Scan A.00h</td> |
|---|
| 1578 | <td>Hybridization A.00h</td> |
|---|
| 1579 | <td>Scanner A</td> |
|---|
| 1580 | <td>Scanning A</td> |
|---|
| 1581 | </tr> |
|---|
| 1582 | <tr> |
|---|
| 1583 | <td>Scan A.24h</td> |
|---|
| 1584 | <td>Hybridization A.24h</td> |
|---|
| 1585 | <td>Scanner A</td> |
|---|
| 1586 | <td>Scanning A</td> |
|---|
| 1587 | </tr> |
|---|
| 1588 | <tr class="shaded"> |
|---|
| 1589 | <td>Scan A.00h (dye-swap)</td> |
|---|
| 1590 | <td>Hybridization A.00h (dye-swap)</td> |
|---|
| 1591 | <td>Scanner A</td> |
|---|
| 1592 | <td>Scanning A</td> |
|---|
| 1593 | </tr> |
|---|
| 1594 | <tr class="shaded"> |
|---|
| 1595 | <td>Scan A.24h (dye-swap)</td> |
|---|
| 1596 | <td>Hybridization A.24h (dye-swap)</td> |
|---|
| 1597 | <td>Scanner A</td> |
|---|
| 1598 | <td>Scanning A</td> |
|---|
| 1599 | </tr> |
|---|
| 1600 | <tr> |
|---|
| 1601 | <td>Affymetrix scan A.1</td> |
|---|
| 1602 | <td>Affymetrix hyb A.1</td> |
|---|
| 1603 | <td>Scanner A</td> |
|---|
| 1604 | <td>Scanning A</td> |
|---|
| 1605 | </tr> |
|---|
| 1606 | <tr> |
|---|
| 1607 | <td>Affymetrix scan A.2</td> |
|---|
| 1608 | <td>Affymetrix hyb A.2</td> |
|---|
| 1609 | <td>Scanner A</td> |
|---|
| 1610 | <td>Scanning A</td> |
|---|
| 1611 | </tr> |
|---|
| 1612 | <tr> |
|---|
| 1613 | <td>Affymetrix scan A.3</td> |
|---|
| 1614 | <td>Affymetrix hyb A.3</td> |
|---|
| 1615 | <td>Scanner A</td> |
|---|
| 1616 | <td>Scanning A</td> |
|---|
| 1617 | </tr> |
|---|
| 1618 | </table> |
|---|
| 1619 | <p> |
|---|
| 1620 | </li> |
|---|
| 1621 | |
|---|
| 1622 | <li> |
|---|
| 1623 | Add images to the scans (TODO - we don't have any images yet): |
|---|
| 1624 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1625 | <tr> |
|---|
| 1626 | <th>Scan</th> |
|---|
| 1627 | <th>Image files</th> |
|---|
| 1628 | </tr> |
|---|
| 1629 | <tr> |
|---|
| 1630 | <td>Scan A.00h</td> |
|---|
| 1631 | <td>-</td> |
|---|
| 1632 | </tr> |
|---|
| 1633 | <tr> |
|---|
| 1634 | <td>Scan A.24h</td> |
|---|
| 1635 | <td>-</td> |
|---|
| 1636 | </tr> |
|---|
| 1637 | <tr class="shaded"> |
|---|
| 1638 | <td>Scan A.00h (dye-swap)</td> |
|---|
| 1639 | <td>-</td> |
|---|
| 1640 | </tr> |
|---|
| 1641 | <tr class="shaded"> |
|---|
| 1642 | <td>Scan A.24h (dye-swap)</td> |
|---|
| 1643 | <td>-</td> |
|---|
| 1644 | </tr> |
|---|
| 1645 | </table> |
|---|
| 1646 | <p> |
|---|
| 1647 | </li> |
|---|
| 1648 | |
|---|
| 1649 | <li> |
|---|
| 1650 | Create raw bioassays: |
|---|
| 1651 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1652 | <tr> |
|---|
| 1653 | <th>Name</th> |
|---|
| 1654 | <th>Platform/Raw data type</th> |
|---|
| 1655 | <th>Array design</th> |
|---|
| 1656 | <th>Protocol</th> |
|---|
| 1657 | <th>Scan</th> |
|---|
| 1658 | <th>Software</th> |
|---|
| 1659 | <th>File(s)</th> |
|---|
| 1660 | </tr> |
|---|
| 1661 | <tr> |
|---|
| 1662 | <td>Raw bioassay A.00h</td> |
|---|
| 1663 | <td>Generic/GenePix</td> |
|---|
| 1664 | <td>Array design A</td> |
|---|
| 1665 | <td>Feature extraction A</td> |
|---|
| 1666 | <td>Scan A.00h</td> |
|---|
| 1667 | <td>Software A</td> |
|---|
| 1668 | <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.gpr</td> |
|---|
| 1669 | </tr> |
|---|
| 1670 | <tr> |
|---|
| 1671 | <td>Raw bioassay A.24h</td> |
|---|
| 1672 | <td>Generic/GenePix</td> |
|---|
| 1673 | <td>Array design A</td> |
|---|
| 1674 | <td>Feature extraction A</td> |
|---|
| 1675 | <td>Scan A.24h</td> |
|---|
| 1676 | <td>Software A</td> |
|---|
| 1677 | <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.gpr</td> |
|---|
| 1678 | </tr> |
|---|
| 1679 | <tr class="shaded"> |
|---|
| 1680 | <td>Raw bioassay A.00h (dye-swap)</td> |
|---|
| 1681 | <td>Generic/GenePix</td> |
|---|
| 1682 | <td>Array design A</td> |
|---|
| 1683 | <td>Feature extraction A</td> |
|---|
| 1684 | <td>Scan A.00h (dye-swap)</td> |
|---|
| 1685 | <td>Software A</td> |
|---|
| 1686 | <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.dyeswap.gpr</td> |
|---|
| 1687 | </tr> |
|---|
| 1688 | <tr class="shaded"> |
|---|
| 1689 | <td>Raw bioassay A.24h (dye-swap)</td> |
|---|
| 1690 | <td>Generic/GenePix</td> |
|---|
| 1691 | <td>Array design A</td> |
|---|
| 1692 | <td>Feature extraction A</td> |
|---|
| 1693 | <td>Scan A.24h (dye-swap)</td> |
|---|
| 1694 | <td>Software A</td> |
|---|
| 1695 | <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.dyeswap.gpr</td> |
|---|
| 1696 | </tr> |
|---|
| 1697 | <tr> |
|---|
| 1698 | <td>Affymetrix raw A.1</td> |
|---|
| 1699 | <td>Affymetrix</td> |
|---|
| 1700 | <td>Affymetrix A</td> |
|---|
| 1701 | <td>Feature extraction A</td> |
|---|
| 1702 | <td>Affymetrix scan A.1</td> |
|---|
| 1703 | <td>Software A</td> |
|---|
| 1704 | <td><i>CEL file</i>: jos1761.cel.bz2</td> |
|---|
| 1705 | </tr> |
|---|
| 1706 | <tr> |
|---|
| 1707 | <td>Affymetrix raw A.2</td> |
|---|
| 1708 | <td>Affymetrix</td> |
|---|
| 1709 | <td>Affymetrix A</td> |
|---|
| 1710 | <td>Feature extraction A</td> |
|---|
| 1711 | <td>Affymetrix scan A.2</td> |
|---|
| 1712 | <td>Software A</td> |
|---|
| 1713 | <td><i>CEL file</i>: jos1762.cel.bz2</td> |
|---|
| 1714 | </tr> |
|---|
| 1715 | <tr> |
|---|
| 1716 | <td>Affymetrix raw A.3</td> |
|---|
| 1717 | <td>Affymetrix</td> |
|---|
| 1718 | <td>Affymetrix A</td> |
|---|
| 1719 | <td>Feature extraction A</td> |
|---|
| 1720 | <td>Affymetrix scan A.3</td> |
|---|
| 1721 | <td>Software A</td> |
|---|
| 1722 | <td><i>CEL file</i>: jos1763.cel.bz2</td> |
|---|
| 1723 | </tr> |
|---|
| 1724 | </table> |
|---|
| 1725 | <p> |
|---|
| 1726 | </li> |
|---|
| 1727 | </ol> |
|---|
| 1728 | |
|---|
| 1729 | <a name="step3"></a> |
|---|
| 1730 | <h3>Third step</h3> |
|---|
| 1731 | <ol> |
|---|
| 1732 | <li> |
|---|
| 1733 | Create experiments: |
|---|
| 1734 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1735 | <tr> |
|---|
| 1736 | <th>Name</th> |
|---|
| 1737 | <th>Raw data type</th> |
|---|
| 1738 | <th>Raw bioassays</th> |
|---|
| 1739 | <th>Experimental factors</th> |
|---|
| 1740 | </tr> |
|---|
| 1741 | <tr> |
|---|
| 1742 | <td>Experiment A</td> |
|---|
| 1743 | <td>GenePix</td> |
|---|
| 1744 | <td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br> |
|---|
| 1745 | Raw bioassay A.24h (dye-swap)</td> |
|---|
| 1746 | <td>Drug resistance, Time, Dye swap</td> |
|---|
| 1747 | </tr> |
|---|
| 1748 | <tr> |
|---|
| 1749 | <td>Affymetrix A</td> |
|---|
| 1750 | <td>Affymetrix</td> |
|---|
| 1751 | <td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td> |
|---|
| 1752 | <td>Drug resistance, Time</td> |
|---|
| 1753 | </tr> |
|---|
| 1754 | </table> |
|---|
| 1755 | <p> |
|---|
| 1756 | </li> |
|---|
| 1757 | |
|---|
| 1758 | <li><a name="inheritannotations"></a> |
|---|
| 1759 | Inherit the annotations from the samples and biosource for each raw bioassay. |
|---|
| 1760 | Use the <i>auto-inherit</i> function that exists on the experiment properties |
|---|
| 1761 | tab. The <i>Status</i> column in <i>Experimental factors</i> table should indicate |
|---|
| 1762 | the number of raw bioassays that is missing a value. Click on this warning to |
|---|
| 1763 | automatically inherit annotations from the parents. Note! The <i>Dye swap</i> |
|---|
| 1764 | annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i> |
|---|
| 1765 | data set doesn't have any parents with annotations. |
|---|
| 1766 | <p> |
|---|
| 1767 | |
|---|
| 1768 | </li> |
|---|
| 1769 | |
|---|
| 1770 | <li> |
|---|
| 1771 | Import GenePix raw data. There are two possible ways to do this: |
|---|
| 1772 | <ol> |
|---|
| 1773 | <li>Manually import to each raw bioassay. |
|---|
| 1774 | <li>Batch import to multiple raw bioassays. |
|---|
| 1775 | </ol> |
|---|
| 1776 | <p> |
|---|
| 1777 | <b>Manual import:</b> Go to the properties tab for each raw bioassay. |
|---|
| 1778 | Click on the <i>Import</i> button and use the auto-detect feature to |
|---|
| 1779 | import the raw data. Use the default configuration values except for |
|---|
| 1780 | those listed in the table below. |
|---|
| 1781 | <p> |
|---|
| 1782 | |
|---|
| 1783 | <b>Batch import:</b> The batch import is started from the |
|---|
| 1784 | properties tab of the <i>experiment</i>. Click on "Import" and |
|---|
| 1785 | use the auto-detect feature with one of the used files. Use the default |
|---|
| 1786 | configuration values except for those listed in the table below. |
|---|
| 1787 | The batch import should import two raw data sets in one go (since it can |
|---|
| 1788 | only work with a single file format at a time and the dye-swap files uses |
|---|
| 1789 | a different file format). Repeat the batch import a second time to import |
|---|
| 1790 | the remaining two raw data sets. |
|---|
| 1791 | <p> |
|---|
| 1792 | |
|---|
| 1793 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1794 | <tr> |
|---|
| 1795 | <th>Parameter</th> |
|---|
| 1796 | <th>Value</th> |
|---|
| 1797 | <th>Mode</th> |
|---|
| 1798 | </tr> |
|---|
| 1799 | <tr> |
|---|
| 1800 | <td>Feature mismatch</td> |
|---|
| 1801 | <td>smart</td> |
|---|
| 1802 | <td>both</td> |
|---|
| 1803 | </tr> |
|---|
| 1804 | <tr> |
|---|
| 1805 | <td>Invalid numeric value</td> |
|---|
| 1806 | <td>null</td> |
|---|
| 1807 | <td>both</td> |
|---|
| 1808 | </tr> |
|---|
| 1809 | <tr> |
|---|
| 1810 | <td>Log file</td> |
|---|
| 1811 | <td>~/import.log</td> |
|---|
| 1812 | <td>batch import</td> |
|---|
| 1813 | </tr> |
|---|
| 1814 | </table> |
|---|
| 1815 | <p> |
|---|
| 1816 | |
|---|
| 1817 | In both cases, the import should produce the same results |
|---|
| 1818 | as in the table below. When using the batch import mode, the |
|---|
| 1819 | detailed information for each raw bioassay is only found in |
|---|
| 1820 | the log file. |
|---|
| 1821 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1822 | <tr> |
|---|
| 1823 | <th>Raw bioassay</th> |
|---|
| 1824 | <th>Raw data file</th> |
|---|
| 1825 | <th>Spots inserted/with null reporter/skipped)</th> |
|---|
| 1826 | <th>Annotations created</th> |
|---|
| 1827 | </tr> |
|---|
| 1828 | <tr> |
|---|
| 1829 | <td>Raw bioassay A.00h</td> |
|---|
| 1830 | <td>genepix.mouse.v4.37k.00h.gpr</td> |
|---|
| 1831 | <td>36,864/632/768</td> |
|---|
| 1832 | <td><i>Dye swap</i>: false</td> |
|---|
| 1833 | </tr> |
|---|
| 1834 | <tr> |
|---|
| 1835 | <td>Raw bioassay A.24h</td> |
|---|
| 1836 | <td>genepix.mouse.v4.37k.24h.gpr</td> |
|---|
| 1837 | <td>36,864/632/768</td> |
|---|
| 1838 | <td><i>Dye swap</i>: false</td> |
|---|
| 1839 | </tr> |
|---|
| 1840 | <tr class="shaded"> |
|---|
| 1841 | <td>Raw bioassay A.00h (dye-swap)</td> |
|---|
| 1842 | <td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td> |
|---|
| 1843 | <td>36,864/632/768</td> |
|---|
| 1844 | <td><i>Dye swap</i>: true</td> |
|---|
| 1845 | </tr> |
|---|
| 1846 | <tr class="shaded"> |
|---|
| 1847 | <td>Raw bioassay A.24h (dye-swap)</td> |
|---|
| 1848 | <td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td> |
|---|
| 1849 | <td>36,864/632/768</td> |
|---|
| 1850 | <td><i>Dye swap</i>: true</td> |
|---|
| 1851 | </tr> |
|---|
| 1852 | </table> |
|---|
| 1853 | <p> |
|---|
| 1854 | |
|---|
| 1855 | </li> |
|---|
| 1856 | |
|---|
| 1857 | <li> |
|---|
| 1858 | Check the experiment overview page. It should display one warnings for the |
|---|
| 1859 | Genepix experiment. The warning is related to a missing biosurce |
|---|
| 1860 | on the reference sample. |
|---|
| 1861 | <p> |
|---|
| 1862 | The Affymetrix experiment gives some more warnings. Most of them are |
|---|
| 1863 | related to not using the project default items, missing protocols |
|---|
| 1864 | and missing hardware. There should also be an error about missing |
|---|
| 1865 | experimental factor values for the <code>Affymetrix.3</code> |
|---|
| 1866 | raw bioassay. It is expected since this comes from the reference sample |
|---|
| 1867 | which doesn't have values for those annotations. |
|---|
| 1868 | <p> |
|---|
| 1869 | |
|---|
| 1870 | Change validation options to reduce the number of warnings: |
|---|
| 1871 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1872 | <tr> |
|---|
| 1873 | <th>Validation option</th> |
|---|
| 1874 | <th>Setting</th> |
|---|
| 1875 | </tr> |
|---|
| 1876 | <tr> |
|---|
| 1877 | <td>Project defaults</td> |
|---|
| 1878 | <td>Set all to <code>Ignore</code></td> |
|---|
| 1879 | </tr> |
|---|
| 1880 | <tr> |
|---|
| 1881 | <td>Missing items</td> |
|---|
| 1882 | <td>Set all to <code>Ignore</code></td> |
|---|
| 1883 | </tr> |
|---|
| 1884 | <tr> |
|---|
| 1885 | <td>Annotations - Missing factor value</td> |
|---|
| 1886 | <td><code>Warning</code></td> |
|---|
| 1887 | </tr> |
|---|
| 1888 | </table> |
|---|
| 1889 | |
|---|
| 1890 | After the changes there should now only be two warnings about the |
|---|
| 1891 | missing factor values. |
|---|
| 1892 | |
|---|
| 1893 | <p> |
|---|
| 1894 | </li> |
|---|
| 1895 | |
|---|
| 1896 | </ol> |
|---|
| 1897 | </li> |
|---|
| 1898 | </ol> |
|---|
| 1899 | |
|---|
| 1900 | <a name="analysis"></a> |
|---|
| 1901 | <h2>6. Analysis tests</h2> |
|---|
| 1902 | <p> |
|---|
| 1903 | Now it is time to analyse the data. The analysis test should be done |
|---|
| 1904 | by both a regular user and a guest. |
|---|
| 1905 | </p> |
|---|
| 1906 | |
|---|
| 1907 | <ol> |
|---|
| 1908 | <li> |
|---|
| 1909 | Activate the <code>Project A</code> project<p> |
|---|
| 1910 | </li> |
|---|
| 1911 | |
|---|
| 1912 | <li> |
|---|
| 1913 | Go to the <code>Experiment A</code> experiment and select |
|---|
| 1914 | the <code>Bioassay sets</code> tab. |
|---|
| 1915 | <p> |
|---|
| 1916 | </li> |
|---|
| 1917 | |
|---|
| 1918 | <li> |
|---|
| 1919 | Create a new root bioassay set: |
|---|
| 1920 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1921 | <tr> |
|---|
| 1922 | <th>Bioassay set name</th> |
|---|
| 1923 | <th>Raw bioassays</th> |
|---|
| 1924 | <th>Formula</th> |
|---|
| 1925 | </tr> |
|---|
| 1926 | <tr> |
|---|
| 1927 | <td>Root bioassay set</td> |
|---|
| 1928 | <td>all</td> |
|---|
| 1929 | <td>Mean FG - Mean BG</td> |
|---|
| 1930 | </tr> |
|---|
| 1931 | </table> |
|---|
| 1932 | Wait for the plug-in to finish. |
|---|
| 1933 | <p> |
|---|
| 1934 | </li> |
|---|
| 1935 | |
|---|
| 1936 | <li> |
|---|
| 1937 | Select the created bioassay set and create a filtered bioassayset: |
|---|
| 1938 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1939 | <tr> |
|---|
| 1940 | <th>Child name</th> |
|---|
| 1941 | <th>Filter preset</th> |
|---|
| 1942 | <th>Expression</th> |
|---|
| 1943 | </tr> |
|---|
| 1944 | <tr> |
|---|
| 1945 | <td>Filtered bioassay set</td> |
|---|
| 1946 | <td>-</td> |
|---|
| 1947 | <td>ch(1) > 0 && ch(2) > 0 && rep('id') != null</td> |
|---|
| 1948 | </tr> |
|---|
| 1949 | </table> |
|---|
| 1950 | Wait for the plug-in to finish. It should report that 136,498 spots remain and |
|---|
| 1951 | that 10,958 spots has been removed. |
|---|
| 1952 | <p> |
|---|
| 1953 | </li> |
|---|
| 1954 | |
|---|
| 1955 | <li> |
|---|
| 1956 | Select the filtered bioassay set and run a normalization plug-in: |
|---|
| 1957 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1958 | <tr> |
|---|
| 1959 | <th>Plugin</th> |
|---|
| 1960 | <th>Parameters</th> |
|---|
| 1961 | </tr> |
|---|
| 1962 | <tr> |
|---|
| 1963 | <td>Normalization: Lowess</td> |
|---|
| 1964 | <td>Accept the default parameters.</td> |
|---|
| 1965 | </tr> |
|---|
| 1966 | </table> |
|---|
| 1967 | Wait for the plug in to finish. It should report that 136,498 spots has been |
|---|
| 1968 | normalized and 0 spots has been removed. |
|---|
| 1969 | <p> |
|---|
| 1970 | </li> |
|---|
| 1971 | |
|---|
| 1972 | <li> |
|---|
| 1973 | Select the normalized bioassay set and check the overview plots and |
|---|
| 1974 | the correction factor plots. Here are four examples: |
|---|
| 1975 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1976 | <tr> |
|---|
| 1977 | <th>Overview plots</th> |
|---|
| 1978 | <th>Correction factor plots</th> |
|---|
| 1979 | </tr> |
|---|
| 1980 | <tr> |
|---|
| 1981 | <td><img src="overview.png"><br><img src="overview.dyeswap.png"></td> |
|---|
| 1982 | <td><img src="correction.png"><br><img src="correction.dyeswap.png"></td> |
|---|
| 1983 | </tr> |
|---|
| 1984 | </table> |
|---|
| 1985 | <p> |
|---|
| 1986 | </li> |
|---|
| 1987 | |
|---|
| 1988 | <li> |
|---|
| 1989 | Try the plot tool with the following plots. Use the <code>Save</code> function |
|---|
| 1990 | to save one them as a file in the BASE file system, and the <code>Download</code> |
|---|
| 1991 | function to download a plot to your computer. |
|---|
| 1992 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 1993 | <tr> |
|---|
| 1994 | <th>Plot type</th> |
|---|
| 1995 | <th>Y-axis preset</th> |
|---|
| 1996 | <th>X-axis preset</th> |
|---|
| 1997 | <th>Other options</th> |
|---|
| 1998 | </tr> |
|---|
| 1999 | <tr> |
|---|
| 2000 | <td>Scatter plot</td> |
|---|
| 2001 | <td>M, log2(ch1 / ch2)</td> |
|---|
| 2002 | <td>A, log10(ch1 * ch2) / 2</td> |
|---|
| 2003 | <td>-</td> |
|---|
| 2004 | </tr> |
|---|
| 2005 | <tr> |
|---|
| 2006 | <td>Histogram plot</td> |
|---|
| 2007 | <td>Count</td> |
|---|
| 2008 | <td>Ratio, ch1 / ch2</td> |
|---|
| 2009 | <td> |
|---|
| 2010 | <table border="0" cellspacing="0" cellpadding="2"> |
|---|
| 2011 | <tr> |
|---|
| 2012 | <td><i>Log scale</i></td> |
|---|
| 2013 | <td>checked</td> |
|---|
| 2014 | </tr> |
|---|
| 2015 | <tr> |
|---|
| 2016 | <td><i>Bin size</i></td> |
|---|
| 2017 | <td>0.1</td> |
|---|
| 2018 | </tr> |
|---|
| 2019 | <tr> |
|---|
| 2020 | <td><i>Annotation</i></td> |
|---|
| 2021 | <td>Time</td> |
|---|
| 2022 | </tr> |
|---|
| 2023 | </table> |
|---|
| 2024 | </td> |
|---|
| 2025 | </tr> |
|---|
| 2026 | </table> |
|---|
| 2027 | <p> |
|---|
| 2028 | Here are two examples: |
|---|
| 2029 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 2030 | <tr> |
|---|
| 2031 | <th>Scatter plot</th> |
|---|
| 2032 | </tr> |
|---|
| 2033 | <tr> |
|---|
| 2034 | <td><img src="scatter.png"></td> |
|---|
| 2035 | </tr> |
|---|
| 2036 | </table> |
|---|
| 2037 | <p> |
|---|
| 2038 | <table class="listing" cellspacing="0" cellpadding="2" border="0"> |
|---|
| 2039 | <tr> |
|---|
| 2040 | <th>Histogram plot</th> |
|---|
| 2041 | </tr> |
|---|
| 2042 | <tr> |
|---|
| 2043 | <td><img src="histogram.png"></td> |
|---|
| 2044 | </tr> |
|---|
| 2045 | </table> |
|---|
| 2046 | <p> |
|---|
| 2047 | </li> |
|---|
| 2048 | |
|---|
| 2049 | </ol> |
|---|
| 2050 | |
|---|
| 2051 | |
|---|
| 2052 | </body> |
|---|
| 2053 | </html> |
|---|
