Changeset 3318 for trunk/doc/src/docbook/userdoc/experiments_analysis.xml
- Timestamp:
- May 10, 2007, 1:40:00 PM (16 years ago)
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trunk/doc/src/docbook/userdoc/experiments_analysis.xml
r3308 r3318 30 30 <?dbhtml dir="analysis"?> 31 31 <title>Experiments and analysis</title> 32 33 <sect1 id="experiments_analysis.scans"> 34 <title>Scans and images</title> 35 <para>TODO</para> 36 </sect1> 37 38 <sect1 id="experiments_analysis.rawbioassay"> 39 <title>Raw bioassays</title> 40 <para>TODO</para> 41 42 <sect2 id="experiments_analysis.rawdatatypes"> 43 <title>Raw data types</title> 44 <para>TODO</para> 45 46 <sect3 id="experiments_analysis.affymetrix"> 47 <title>Affymetrix data</title> 48 <para>TODO</para> 49 </sect3> 50 51 </sect2> 52 53 <sect2 id="experiments_analysis.spotimages"> 54 <title>Spot images</title> 55 <para>TODO</para> 56 </sect2> 57 58 </sect1> 59 60 <sect1 id="experiments_analysis.experiments"> 61 <title>Experiments</title> 62 <para>TODO</para> 63 64 <sect2 id="experiments_analysis.experimentoverview"> 65 <title>Experiment overview</title> 66 67 <para> 68 With the <guilabel>Experiment overview</guilabel> 69 function you can get an overview of all hybridizations, 70 extracts, samples, annotations, etc. used in an 71 experiment. The overview includes a lot of checks 72 that validates your experimental setup for missing 73 or possibly incorrect information. 74 </para> 75 76 <para> 77 You can access the overview of an experiment by navigating 78 to the single-item view of the experiment you are interested in. 79 Then, switch to the <guilabel>Overview</guilabel> tab that 80 is present on that page. Here is an example of what is displayed: 81 </para> 82 83 <figure id="experiments_analysis.figures.experimentoverview"> 84 <title>The experiment overview</title> 85 <screenshot> 86 <mediaobject> 87 <imageobject><imagedata 88 fileref="figures/experiment_overview.png" format="PNG" 89 /></imageobject> 90 </mediaobject> 91 </screenshot> 92 </figure> 93 94 <helptext external_id="experiment.overview " 95 title="Experiment overview"> 96 <para> 97 The page is divided into three sections: 98 </para> 99 100 <itemizedlist> 101 <listitem> 102 <para> 103 To the left is a tree displaying all items 104 in the experiment and how they are linked to 105 each other. 106 </para> 107 </listitem> 108 109 <listitem> 110 <para> 111 The lower right shows a list of warnings and error 112 messages that was found when validating the experiment. 113 <nohelp> 114 In the example you can see that we have failed to 115 specify a value for the <guilabel>Temperature</guilabel> 116 protocol parameter for one of the samples. 117 </nohelp> 118 </para> 119 </listitem> 120 121 <listitem> 122 <para> 123 The upper right shows information about the 124 currently selected item in the tree. This part also 125 contains more information errors or warnings for this 126 item. It may also present you with one or more suggestions 127 about how to fix the problem and with a link that 128 takes you to the most probable location where you can fix 129 the error or warning. 130 </para> 131 132 <note> 133 <title>No links?</title> 134 If you don't have permission to change things no links 135 will be shown. 136 </note> 137 138 </listitem> 139 140 </itemizedlist> 141 142 <seeother> 143 <other external_id="experiment.overview.validationoptions" 144 >Validation options</other> 145 <other external_id="experiment.overview.fixfailures" 146 >How to fix validation failures</other> 147 </seeother> 148 149 </helptext> 150 151 <sect3 id="experiments_analysis.validationoptions"> 152 <title>Validation options</title> 153 <para> 154 Click on the <guibutton>Validation options</guibutton> 155 button in the toolbar to open the <guilabel>Validation 156 options</guilabel> dialog. 157 </para> 158 159 <figure id="experiments_analysis.figures.validationoptions"> 160 <title>Validation options</title> 161 <screenshot> 162 <mediaobject> 163 <imageobject><imagedata 164 fileref="figures/validation_options.png" format="PNG" 165 /></imageobject> 166 </mediaobject> 167 </screenshot> 168 </figure> 169 170 <helptext external_id="experiment.overview.validationoptions" 171 title="Validation options"> 172 <para> 173 The validation procedure is highly 174 configurable and you can select what you want to 175 ignore, or something should be displayed as an error 176 or warning. 177 </para> 178 179 <variablelist> 180 <varlistentry> 181 <term><guilabel>Presets</guilabel></term> 182 <listitem> 183 <para> 184 The list contains predefined and 185 user defined validation options. 186 Use the <guibutton>Save as…</guibutton> 187 button to save the current options as a user defined 188 preset. The <guibutton>Remove…</guibutton> 189 button is used to remove the currently selected 190 preset. Predefined presets can't be deleted. 191 </para> 192 </listitem> 193 </varlistentry> 194 195 <varlistentry> 196 <term><guilabel>Project defaults</guilabel></term> 197 <listitem> 198 <para> 199 The options in this section are used to check 200 if your experiment uses the same values as set 201 by the project default values of the currently active 202 project<nohelp> 203 (see <xref linkend="project_permission.projects" />)</nohelp>. 204 If no project is active or if the active project doesn't 205 have default values these options are ignored. 206 </para> 207 </listitem> 208 209 </varlistentry> 210 211 <varlistentry> 212 <term><guilabel>Missing items</guilabel></term> 213 <listitem> 214 <para> 215 The options in this section are used to check if 216 you have specified values for optional items. 217 For example, there is an option that warns you if 218 you havn't specified a protocol. 219 </para> 220 </listitem> 221 </varlistentry> 222 223 <varlistentry> 224 <term><guilabel>Annotations</guilabel></term> 225 <listitem> 226 <para> 227 The options in this section are used to check 228 problems related to annotations. The most 229 important ones are listed here: 230 </para> 231 232 <itemizedlist> 233 <listitem> 234 <simpara> 235 <emphasis>Missing MIAME annotation value</emphasis>: 236 Checks that you have specified values 237 for all annotations marked as 238 <guilabel>Required for MIAME</guilabel>. 239 </simpara> 240 </listitem> 241 242 <listitem> 243 <simpara> 244 <emphasis>Missing factor value</emphasis>: 245 Checks that you have specified values for 246 all annotations used as experimental factors in 247 the experiment. 248 </simpara> 249 </listitem> 250 251 <listitem> 252 <simpara> 253 <emphasis>Missing parameter value</emphasis>: 254 Checks that you have specified values 255 for all protocol parameters. 256 </simpara> 257 </listitem> 258 259 <listitem> 260 <simpara> 261 <emphasis>Annotation is protocol parameter</emphasis>: 262 Checks if an item has been annotated with a 263 an annotation that is actually a protocol parameter. 264 </simpara> 265 </listitem> 266 267 <listitem> 268 <simpara> 269 <emphasis>Annotation has invalid value</emphasis>: 270 Checks if annotation values are correct with 271 respect to the rules given by the annotation type. 272 This might include numeric values that are outside 273 the valid range, or values not in the list 274 of allows values for an enumerated annotation type. 275 </simpara> 276 </listitem> 277 278 <listitem> 279 <simpara> 280 <emphasis>Inheriting annotation from non-parent</emphasis>: 281 Checks if inherited annotations really comes from a 282 parent item. This might happen if you rearrange 283 parent-child relationship because you found that 284 they were incorrectly linked. 285 </simpara> 286 </listitem> 287 </itemizedlist> 288 289 290 </listitem> 291 </varlistentry> 292 293 <varlistentry> 294 <term><guilabel>Denied access</guilabel></term> 295 <listitem> 296 <para> 297 The options in this section are used to 298 check if you don't have access (read permission) 299 to an item in the experiment hierarchy. If this 300 happens the validation can't proceed in that branch. 301 This might mask other validation problems. 302 </para> 303 </listitem> 304 </varlistentry> 305 306 <varlistentry> 307 <term><guilabel>Other</guilabel></term> 308 <listitem> 309 <para> 310 This section collects options that doesn't fit 311 into any of the other sections. The most 312 important options are: 313 </para> 314 315 <itemizedlist> 316 <listitem> 317 <simpara> 318 <emphasis>Array deign mismatch</emphasis>: 319 Checks if the array design specified for 320 a raw bioassay is the same array design 321 specified for the hybridization. 322 </simpara> 323 </listitem> 324 325 <listitem> 326 <simpara> 327 <emphasis>Multiple array designs</emphasis>: 328 Checks if all raw bioassays use the 329 same array design or not. 330 </simpara> 331 </listitem> 332 333 <listitem> 334 <simpara> 335 <emphasis>Incorrect number of labled extracts</emphasis>: 336 Checks if the number of labeled extracts 337 match the number of channels for the experiment. 338 </simpara> 339 </listitem> 340 341 <listitem> 342 <simpara> 343 <emphasis>Non-unique name</emphasis>: 344 Checks if two items of the same type 345 have the same name. A unique name if important 346 when exporting data in Tab2Mage format. 347 </simpara> 348 </listitem> 349 350 <listitem> 351 <simpara> 352 <emphasis>Circular reference to pooled item</emphasis>: 353 If you have used pooling, checks that no 354 circular references have been created. 355 </simpara> 356 </listitem> 357 358 </itemizedlist> 359 360 </listitem> 361 </varlistentry> 362 363 </variablelist> 364 365 <para> 366 Click on the <guibutton>Save</guibutton> button 367 to use the current settings. The display will 368 automatically refresh itself. 369 </para> 370 371 </helptext> 372 373 <helptext external_id="experiment.overview.validationoptions.savepreset" 374 title="Save preset" webonly="1"> 375 376 <para> 377 Saves all validation options as a preset. 378 </para> 379 380 <variablelist> 381 <varlistentry> 382 <term><guilabel>Name</guilabel></term> 383 <listitem> 384 <para> 385 The name of the preset. The name must be unique 386 and if a preset with the same name already exists 387 you will be asked if you want to overwrite it or not. 388 </para> 389 </listitem> 390 </varlistentry> 391 </variablelist> 392 393 <para> 394 Click on the <guibutton>Save</guibutton> button 395 to save the preset or <guibutton>Cancel</guibutton> 396 to abort. 397 </para> 398 </helptext> 399 400 </sect3> 401 402 <sect3 id="experiments_analysis.fixfailures"> 403 <title>Fixing validation failures</title> 404 <helptext external_id="experiment.overview.fixfailures" 405 title="How to fix validation failures"> 406 407 <para> 408 The experiment overview includes a function that allows 409 you to quickly fix most of the problems found during the 410 validation. The easiest way to use the function is: 411 </para> 412 413 <orderedlist> 414 <listitem> 415 <simpara> 416 Click on an error or warning in the list of failures in 417 the lower right 418 pane. The tree in the left pane and the item overview in the 419 top right pane will automatically be updated to show the 420 exact location of the faulty item. 421 </simpara> 422 </listitem> 423 <listitem> 424 <simpara> 425 The upper right pane should contain a list labeled 426 <guilabel>Failure details</guilabel> with more information 427 about each failure and also one or more suggestions for fixing 428 the problem. For example, a failure due to a missing item 429 should suggest that you add or select an item. 430 </simpara> 431 </listitem> 432 433 <listitem> 434 <simpara> 435 The suggestions should also have links that takes 436 you to an edit view where you can do the changes. 437 </simpara> 438 </listitem> 439 440 <listitem> 441 <simpara> 442 After saving the changes you must click on the 443 <guibutton>Revalidate</guibutton> button to update 444 interface. If you want, you can fix more than one 445 failure before clicking on the button. 446 </simpara> 447 </listitem> 448 449 </orderedlist> 450 451 </helptext> 452 </sect3> 453 454 </sect2> 455 456 <sect2 id="experiments_analysis.magexport"> 457 <title>Tab2Mage export</title> 458 <para>TODO</para> 459 </sect2> 460 461 462 </sect1> 463 464 <sect1 id="experiments_analysis.analysis"> 465 <title>Analysing data within BASE</title> 466 <para>TODO</para> 467 468 <sect2 id="experiments_analysis.bioassaysets"> 469 <title>Transformations and bioassay sets</title> 470 <para>TODO</para> 471 472 <sect3 id="experiments_analysis.rootbioassayset"> 473 <title>The root bioassay set</title> 474 <para>TODO</para> 475 </sect3> 476 477 <sect3 id="experiments_analysis.overviewplots"> 478 <title>Overview plots</title> 479 <para>TODO</para> 480 </sect3> 481 482 </sect2> 483 484 <sect2 id="experiments_analysis.filtering"> 485 <title>Filtering data</title> 486 <para>TODO</para> 487 488 <sect3 id="experiments_analysis.formulas"> 489 <title>Formulas</title> 490 <para>TODO</para> 491 492 </sect3> 493 </sect2> 494 495 <sect2 id="experiments_analysis.normalization"> 496 <title>Normalizing data</title> 497 <para>TODO</para> 498 499 </sect2> 500 501 <sect2 id="experiments_analysis.plugins"> 502 <title>Other analysis plugins</title> 503 <para>TODO</para> 504 505 </sect2> 506 507 508 <sect2 id="experiments_analysis.plotter"> 509 <title>Plot tool</title> 510 <para>TODO</para> 511 512 <sect3 id="experiments_analysis.scatterplot"> 513 <title>Scatter plots</title> 514 <para>TODO</para> 515 </sect3> 516 517 <sect3 id="experiments_analysis.histogramplot"> 518 <title>Histogram plots</title> 519 <para>TODO</para> 520 </sect3> 521 522 <sect3 id="experiments_analysis.filterplot"> 523 <title>Filtering plots</title> 524 <para>TODO</para> 525 </sect3> 526 527 <sect3 id="experiments_analysis.saveplot"> 528 <title>Save plots</title> 529 <para>TODO</para> 530 </sect3> 531 532 </sect2> 533 534 <sect2 id="experiments_analysis.explorer"> 535 <title>Experiment explorer</title> 536 <para>TODO</para> 537 538 <sect3 id="experiments_analysis.explorer.reporterview"> 539 <title>Reporter view</title> 540 <para>TODO</para> 541 </sect3> 542 543 <sect3 id="experiments_analysis.explorer.reportersearch"> 544 <title>Reporter search</title> 545 <para>TODO</para> 546 </sect3> 547 548 </sect2> 549 550 </sect1> 551 552 <sect1 id="experiments_analysis.mev"> 553 <title>Analysing data with Multiexperiment Viewer (MeV)</title> 554 <para>TODO</para> 555 </sect1> 556 557 32 <include file="scans_images.xml"/> 33 <include file="rawbioassays.xml"/> 34 <include file="experiments.xml"/> 35 <include file="analyse_in_base.xml"/> 36 <include file="analyse_mev.xml"/> 558 37 </chapter>
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