Difference between revisions of "Context sensitive help pages"
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Error Message Help Pages
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| − | <div style="text-align: left;">This is a listing of the context sensitive help buttons needed.<br /><br />1) Create a page in the Wiki named the same as the code key<br />2) Fill it with relevant content even if its a duplication (orcondensed form) of user manual content.<br />3) Do <span style="font-weight: bold;">not </span>add these pages to the navigation menu<br /><br /><br /><br /> | + | <div style="text-align: left;"> |
| + | <h1>Error Message Help Pages<br /></h1> | ||
| + | <br /> | ||
| + | <table cellspacing="1" cellpadding="1" border="1" align="" style="width: 702px; height: 263px;" summary=""> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td style="text-align: center;">ERROR CODE #<br /></td> | ||
| + | <td style="text-align: center;">DESCRIPTION</td> | ||
| + | <td style="text-align: center;">ENTER URL AFTER CREATING</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>error_1001</td> | ||
| + | <td>None of the gene sets passed the size thresholds</td> | ||
| + | <td> Done.</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>error_1002<br /></td> | ||
| + | <td>Chip parameter must be specified as you asked to analyze in the space of gene symbols. Chip is used to collapse probes into symbols.<br /></td> | ||
| + | <td> Done.<br />Suggestions:<br />Analyze in gene symbol space on: Pick the chip that corresponds to probe identifiers used in your expression dataset. This chip annotation will be used to automatically map your dataset into gene symbols<br /><br />Analyze in native space: You no longer will be required to enter a chip parameter. Use this option only if your dataset and gene sets already match (i.e no symbol conversions will be done)</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td style="vertical-align: top;">error_1006</td> | ||
| + | <td style="vertical-align: top;"> Signal2Noise or tTest requires that you have at least two samples for each phenotype</td> | ||
| + | <td style="vertical-align: top;">**likely to be changing**</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> error_1010</td> | ||
| + | <td>As the phenotype choosen was categorical, only categorical metrics are allowed. Got: " + metric.getName(), 1010 <br /></td> | ||
| + | <td>Done.<br /> list of categ metrics from the chooser<br /></td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> error_1011</td> | ||
| + | <td>As the phenotype choosen was continuous, only continuous metrics are allowed. Got: " + metric.getName(), 1010 <br /></td> | ||
| + | <td>Done.<br /> list of cont metrics from the chooser</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | |||
| + | <h1> </h1> | ||
| + | <h1>Help Buttons</h1> | ||
| + | This is a listing of the context sensitive help buttons needed.<br /><br />1) Create a page in the Wiki named the same as the code key<br />2) Fill it with relevant content even if its a duplication (orcondensed form) of user manual content.<br />3) Do <span style="font-weight: bold;">not </span>add these pages to the navigation menu<br /><br /><span style="color: rgb(0, 0, 255);">Code keys are now bookmarks in the doc (periods replace with underscores).<br />Root is http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html.</span><br /><span style="color: rgb(255, 0, 0);"> </span><br /><br /> | ||
<table cellspacing="1" cellpadding="1" border="1" align="" summary="" style="width: 735px; height: 818px;"> | <table cellspacing="1" cellpadding="1" border="1" align="" summary="" style="width: 735px; height: 818px;"> | ||
<tbody> | <tbody> | ||
| Line 24: | Line 64: | ||
<tr> | <tr> | ||
<td>grp</td> | <td>grp</td> | ||
| − | <td> | + | <td>meaning of the grp parameter<br /></td> |
| − | <td> </td> | + | <td> where's this help button?<br /><span style="color: rgb(0, 0, 255);">In places where one can choose a single gene set <span style="color: rgb(255, 102, 0);">Not used in app; no help</span></span><br /></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>res</td> | <td>res</td> | ||
<td>meaning of the res parameter <br /></td> | <td>meaning of the res parameter <br /></td> | ||
| − | <td> </td> | + | <td> where's this help button?<br />The dataset in GSEA for example (any place where <span style="color: rgb(0, 0, 255);">a dataset is needed, the parameter is called -res) <span style="color: rgb(255, 102, 0);">Not used in app; no help</span><br /></span></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 85: | Line 125: | ||
<td>xtools.gsea.Gsea</td> | <td>xtools.gsea.Gsea</td> | ||
<td>help for the gsea tool<br /></td> | <td>help for the gsea tool<br /></td> | ||
| − | <td> | + | <td><br /></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>xtools.gsea.GseaPreranked</td> | <td>xtools.gsea.GseaPreranked</td> | ||
<td> help for the gsea preranked tool<br /></td> | <td> help for the gsea preranked tool<br /></td> | ||
| − | <td> | + | <td><br /></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>xtools.munge.CollapseDataset <br /></td> | <td>xtools.munge.CollapseDataset <br /></td> | ||
<td>help for the collapse dataset tool <br /></td> | <td>help for the collapse dataset tool <br /></td> | ||
| − | <td> | + | <td> </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>xtools.chip2chip.Chip2Chip <br /></td> | <td>xtools.chip2chip.Chip2Chip <br /></td> | ||
<td>help for the chip2 chip tool <br /></td> | <td>help for the chip2 chip tool <br /></td> | ||
| − | <td> | + | <td><br /></td> |
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</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
| − | <br /><br /><br /><br /></div> | + | <br /><br /><br /><br /><br /></div> |
Latest revision as of 09:36, 3 October 2006
Error Message Help Pages
| ERROR CODE # |
DESCRIPTION | ENTER URL AFTER CREATING |
| error_1001 | None of the gene sets passed the size thresholds | Done. |
| error_1002 |
Chip parameter must be specified as you asked to analyze in the space of gene symbols. Chip is used to collapse probes into symbols. |
Done. Suggestions: Analyze in gene symbol space on: Pick the chip that corresponds to probe identifiers used in your expression dataset. This chip annotation will be used to automatically map your dataset into gene symbols Analyze in native space: You no longer will be required to enter a chip parameter. Use this option only if your dataset and gene sets already match (i.e no symbol conversions will be done) |
| error_1006 | Signal2Noise or tTest requires that you have at least two samples for each phenotype | **likely to be changing** |
| error_1010 | As the phenotype choosen was categorical, only categorical metrics are allowed. Got: " + metric.getName(), 1010 |
Done. list of categ metrics from the chooser |
| error_1011 | As the phenotype choosen was continuous, only continuous metrics are allowed. Got: " + metric.getName(), 1010 |
Done. list of cont metrics from the chooser |
Help Buttons
This is a listing of the context sensitive help buttons needed.
1) Create a page in the Wiki named the same as the code key
2) Fill it with relevant content even if its a duplication (orcondensed form) of user manual content.
3) Do not add these pages to the navigation menu
Code keys are now bookmarks in the doc (periods replace with underscores).
Root is http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html.
| CODE KEY | DESCRIPTION | ENTER URL AFTER CREATING |
| chip | meaning of the chip parameter | |
| chip_target |
meaning of the chip_target parameter | |
| chip_source | meaning of the chip_source parameter | |
| grp | meaning of the grp parameter |
where's this help button? In places where one can choose a single gene set Not used in app; no help |
| res | meaning of the res parameter |
where's this help button? The dataset in GSEA for example (any place where a dataset is needed, the parameter is called -res) Not used in app; no help |
| gmx | meaning of the gmx parameter |
|
| cls | meaning of the cls parameter |
|
| on_the_fly_phenotype | ctx help for the on the fly template chooser |
|
| gene_profile_phenotype | ctx help for the gene profile chooser |
|
| gsea_preferences_widget |
ctx help for gsea prefs screen |
|
| post_hoc |
main help the leadingf edge screen |
|
| msigdb_browser |
main help for the gene sets browser |
|
| xtools.gsea.Gsea | help for the gsea tool |
|
| xtools.gsea.GseaPreranked | help for the gsea preranked tool |
|
| xtools.munge.CollapseDataset |
help for the collapse dataset tool |
|
| xtools.chip2chip.Chip2Chip |
help for the chip2 chip tool |
