Context sensitive 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 /><span style="color: rgb(0, 0, 255);">Code keys are now bookmarks in the doc. Root is http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm.</span><br /><span style="color: rgb(255, 0, 0);">Two I have questions on, so are not yet bookmarked. </span><br /><br />
<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 /><span style="color: rgb(0, 0, 255);">Code keys are now bookmarks in the doc. Root is http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm.</span><br /><span style="color: rgb(255, 0, 0);">Two I have questions on, so are not yet bookmarked. </span><br /><br />
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             <td>grp</td>
             <td>grp</td>
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             <td>&nbsp;meaning of the grp parameter<br /></td>
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             <td>meaning of the grp parameter<br /></td>
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             <td>&nbsp;where's this help button?<br /></td>
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             <td>&nbsp;where's this help button?<br /><span style="color: rgb(0, 0, 255);">In places where one can choose a single gene set</span><br /></td>
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             <td>res</td>
             <td>res</td>
             <td>meaning of the res parameter <br /></td>
             <td>meaning of the res parameter <br /></td>
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             <td>&nbsp;where's this help button?</td>
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             <td>&nbsp;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></td>
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<h2>Help pages for common error messages</h2>
<h2>Help pages for common error messages</h2>
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Revision as of 22:20, 3 April 2006

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. Root is http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm.
Two I have questions on, so are not yet bookmarked.

<tbody> </tbody>
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
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)
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
GSEAUserGuide.htm#Run_GSEA_Page
xtools.gsea.GseaPreranked  help for the gsea preranked tool
 GSEAUserGuide.htm#_Toc131302100
xtools.munge.CollapseDataset
help for the collapse dataset tool
 GSEAUserGuide.htm#_Toc131302101
xtools.chip2chip.Chip2Chip
help for the chip2 chip tool
 GSEAUserGuide.htm#_Toc131302097




Help pages for common error messages



<tbody> </tbody>
ERROR CODE #
DESCRIPTION ENTER URL AFTER CREATING
error_1001 None of the gene sets passed the size thresholds  
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.
 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_1010 As the phenotype choosen was categorical, only categorical metrics are allowed. Got: " + metric.getName(), 1010
 list of categ metrics from the chooser
 error_1011 As the phenotype choosen was continuous, only continuous metrics are allowed. Got: " + metric.getName(), 1010
  list of cont metrics from the chooser




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