Changeset 3362
- Timestamp:
- May 22, 2007, 12:11:05 PM (16 years ago)
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trunk/doc/src/docbook/userdoc/experiments.xml
r3318 r3362 29 29 <sect1 id="experiments_analysis.experiments"> 30 30 <title>Experiments</title> 31 <para>TODO</para> 31 <para> 32 Experiments are the starting point for analysis. When you have 33 uploaded and imported your raw data, collected and registered all 34 information and annotations about samples, hybridizations, and other 35 items, it is time to collect everything in an experiment. 36 </para> 37 38 <para> 39 To create a new experiment you can either mark one ore more 40 raw biossays on the raw bioassays list view and use the 41 <guibutton>New experiment</guibutton> button. You can also 42 create a new experiment from the experiments list view. 43 </para> 32 44 33 45 <sect2 id="experiments_analysis.experiment.properties"> 34 46 <title>Experiment properties</title> 35 47 36 <para>TODO</para> 48 <figure id="experiments_analysis.figures.experiment_properties"> 49 <title>Create experiment</title> 50 <screenshot> 51 <mediaobject> 52 <imageobject><imagedata 53 fileref="figures/experiment_properties.png" format="PNG" 54 /></imageobject> 55 </mediaobject> 56 </screenshot> 57 </figure> 58 59 60 <helptext external_id="experiment.edit" title="Edit experiment"> 61 62 <variablelist> 63 <varlistentry> 64 <term><guilabel>Name</guilabel></term> 65 <listitem> 66 <para> 67 The name of the experiment. 68 </para> 69 </listitem> 70 </varlistentry> 71 72 <varlistentry> 73 <term><guilabel>Raw data type</guilabel></term> 74 <listitem> 75 <para> 76 The raw data type to use in the experiment. All raw bioassays 77 must have raw data with this type. 78 </para> 79 </listitem> 80 </varlistentry> 81 82 <varlistentry> 83 <term><guilabel>Directory</guilabel></term> 84 <listitem> 85 <para> 86 A directory in the BASE file system where plug-ins 87 can save files that are generated during the analysis. 88 This is optional and if not given the plug-ins must ask 89 about a directory each time they need it. Use the 90 <guibutton>Select</guibutton> button to browse the file system 91 or create a new directory. 92 </para> 93 </listitem> 94 </varlistentry> 95 96 <varlistentry> 97 <term><guilabel>Raw bioassays</guilabel></term> 98 <listitem> 99 <para> 100 The raw bioassays you want to analyze in this experiment. If 101 you created the experiment from the raw bioassays list the 102 selected raw bioassays are already filled in. Use the 103 <guibutton>Add raw bioassays</guibutton> button to add more 104 raw bioassays or the <guibutton>Remove</guibutton> button 105 to remove the selected raw bioassays from the list. 106 </para> 107 </listitem> 108 </varlistentry> 109 110 <varlistentry> 111 <term><guilabel>Description</guilabel></term> 112 <listitem> 113 <para> 114 A description of the experiment. 115 </para> 116 </listitem> 117 </varlistentry> 118 119 </variablelist> 120 121 <para> 122 Click on the <guibutton>Save</guibutton> button to save the 123 changes or on <guibutton>Cancel</guibutton> to abort. 124 </para> 125 126 <seeother> 127 <other external_id="experiment.edit.publication">Publication</other> 128 <other external_id="experiment.edit.factors">Experimental factors</other> 129 </seeother> 130 </helptext> 131 132 <sect3 id="experiments_analysis.experiment.publication"> 133 <title>The publication tab</title> 134 135 <helptext external_id="experiment.edit.publication" 136 title="Experiment publication"> 137 138 <para> 139 On this tab you can enter information about a publication 140 that is the result of the experiment. All of this information 141 is optional. 142 </para> 143 144 <variablelist> 145 <varlistentry> 146 <term><guilabel>PubMedId</guilabel></term> 147 <listitem> 148 <para> 149 The ID of the publication in the 150 <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.html" 151 >PubMed</ulink> database. 152 </para> 153 </listitem> 154 </varlistentry> 155 <varlistentry> 156 <term><guilabel>Title</guilabel></term> 157 <listitem> 158 <para> 159 The title of the publication. 160 </para> 161 </listitem> 162 </varlistentry> 163 <varlistentry> 164 <term><guilabel>Publication date</guilabel></term> 165 <listitem> 166 <para> 167 The date the article was published. Use the 168 <guibutton>Calendar</guibutton> button to select 169 a date from a popup window. 170 </para> 171 </listitem> 172 </varlistentry> 173 <varlistentry> 174 <term><guilabel>Abstract</guilabel></term> 175 <listitem> 176 <para> 177 The article abstract. 178 </para> 179 </listitem> 180 </varlistentry> 181 <varlistentry> 182 <term><guilabel>Experiment design</guilabel></term> 183 <listitem> 184 <para> 185 An explanation of the experiment design. 186 </para> 187 </listitem> 188 </varlistentry> 189 <varlistentry> 190 <term><guilabel>Experiment type</guilabel></term> 191 <listitem> 192 <para> 193 A description of the experiment type. 194 </para> 195 </listitem> 196 </varlistentry> 197 <varlistentry> 198 <term><guilabel>Affiliations</guilabel></term> 199 <listitem> 200 <para> 201 Partners and other related organisations that 202 have helped with the experiment. 203 </para> 204 </listitem> 205 </varlistentry> 206 <varlistentry> 207 <term><guilabel>Authors</guilabel></term> 208 <listitem> 209 <para> 210 The list of authors of the publication. 211 </para> 212 </listitem> 213 </varlistentry> 214 <varlistentry> 215 <term><guilabel>Publication</guilabel></term> 216 <listitem> 217 <para> 218 The body text of the publication. 219 </para> 220 </listitem> 221 </varlistentry> 222 </variablelist> 223 224 <para> 225 Click on the <guibutton>Save</guibutton> button to save the 226 changes or on <guibutton>Cancel</guibutton> to abort. 227 </para> 228 229 <seeother> 230 <other external_id="experiment.edit">Experiment properties</other> 231 <other external_id="experiment.edit.factors">Experimental factors</other> 232 </seeother> 233 </helptext> 234 </sect3> 37 235 38 236 </sect2> 237 238 <sect2 id="experiments_analysis.experiment.factors"> 239 <title>Experimental factors</title> 240 241 <helptext external_id="experiment.edit.factors" 242 title="Experimental factors"> 243 244 <para> 245 The experimental factors of an experiment are the variables 246 you are studying in the experiment. Typically the value of 247 an experimental factor is varied between samples or group of samples. 248 Different treatment methods is an example of an experimental factor. 249 </para> 250 251 <para> 252 In the BASE world an experimental factor is the same as an annotation 253 type. Since you probably have lots of annotations on your items that are not 254 relevant for the experiment you must select the annotations types 255 that should make up the experimental factors of the experiment. 256 </para> 257 258 <para> 259 Use the <guibutton>Add annotation types</guibutton> button to 260 select the annotation types that should be used as experimental 261 factors. The <guibutton>Remove</guibutton> button removes the 262 selected annotation types. 263 </para> 264 265 <para> 266 Click on the <guibutton>Save</guibutton> button to save the 267 changes or on <guibutton>Cancel</guibutton> to abort. 268 </para> 269 270 <para> 271 To be able to use the values of the experimental factors 272 in the analysis of your data the values must be accessible 273 from the raw bioassays. Since most of your annotations are 274 probably made at the sample level the raw bioassays must 275 inherit those annotations. 276 <nohelp>Read <xref linkend="annotations" /> 277 for more information about this.</nohelp> 278 </para> 279 280 <tip> 281 <para> 282 Use the <guilabel>Experiment overview</guilabel> function to 283 verify that all your raw bioassays has been annotated or 284 inherited values for all experimental factors. If not, you 285 should do that before starting with the analysis. 286 </para> 287 </tip> 288 289 <seeother> 290 <other external_id="experiment.edit">Experiment properties</other> 291 <other external_id="experiment.edit.publication">Publication</other> 292 <other external_id="experiment.overview">Experiment overview</other> 293 <other external_id="annotations.edit.inerited">Inherit annotations</other> 294 </seeother> 295 296 </helptext> 297 </sect2> 298 39 299 40 300 <sect2 id="experiments_analysis.experiment.overview"> … … 68 328 </figure> 69 329 70 <helptext external_id="experiment.overview 330 <helptext external_id="experiment.overview" 71 331 title="Experiment overview"> 72 332 <para>
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