Gsea enhancements

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<p>&nbsp;<span style="font-weight: bold;">Notes</span>: <br />1. By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag.</p>
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<h1><span style="font-weight: bold;">Notes</span></h1>
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<p>2. Rejected/Revised bugs removed from this page: see [http://wwwdev.broad.mit.edu/gsea/doc/GSEA_enh_history.doc GSEA_enh_history.doc].</p>
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<p>1. By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag.</p>
 +
<p>2. Rejected/Revised bugs removed from this page: see [http://wwwdev.broad.mit.edu/gsea/doc/GSEA_enh_history.doc GSEA_enh_history.doc].<br /></p>
 +
<h1>Enhancements/Bugs</h1>
<p><span style="font-weight: bold;">Beta testing 4/18:</span><br />1. Created a tiny dataset with 4 samples; create phenotype on the fly with 1 sample in ClassA and 3 in ClassB; got this error. If I create phenotype on the fly with 2 samples in each class, life is good.<br /><br />Nan hit score for feature: TACC2 ---- Stack Trace ---- # of exceptions: 1 ------Nan hit score for feature: TACC2------ java.lang.IllegalStateException: Nan hit score for feature: TACC2 at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore_all_modes(KSCore.java:137) at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore(KSCore.java:46) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:377) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:292) at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156) at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130) at xtools.gsea.Gsea.execute_one(Gsea.java:152) at xtools.gsea.Gsea.execute(Gsea.java:104) at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:464) at java.lang.Thread.run(Unknown Source) 2. From the command line, gene set names have to be case sensitive. They should be case INsensitive. (Tested using xtools.gsea.LeadingEdgeTool, where -gsets is comma-separated list of gene set names.)<br /><br /><span style="color: rgb(255, 102, 0);">If 2 samples or less in a class then signal to noise, tTest will not work. Need to use ratio of means.</span><br /><span style="color: rgb(255, 0, 255);">If you want to trap the error and provide a &quot;standard&quot; error box with a help button; I'm happy to write wiki text for it. </span><br /><br /><span style="font-weight: bold;">Found 4/4:</span><br /><br />1. Specify Bhattacharyya with Continous pheno, should get error 1011 (get hardcoded error). Metric for ranking genes parameter.<br /><br /><span style="color: rgb(255, 102, 0);">Bhattacharyya is a continuous metric so isnt this correct?</span><br /><span style="color: rgb(255, 0, 0);">When I run Bhattacharyya with a continuous phenotype I get the following error (no error help button):</span><br /><br />&nbsp;Tool execution error<br />&nbsp;Message: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50<br />&nbsp;This metric can only be used with 2 class comparisons<br /><br />-------------------------------------------------------------<br />java.lang.RuntimeException: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50<br />&nbsp;This metric can only be used with 2 class comparisons<br />&nbsp;&nbsp;&nbsp; at edu.mit.broad.genome.alg.VectorSplitter._barf_not_biphasic(VectorSplitter.java:71)....<br /><br />2. Specify Pearson with Categorical, should get error 1010 (get hardcoded error). Metric for ranking genes parameter.<br /><br /><span style="color: rgb(255, 102, 0);">Pearson is allowed for categorical &amp; continuous</span><br /><span style="color: rgb(255, 0, 0);">When I run Pearson with a Categorical phenotype, I get the following error (no help button); now that I look more closely, it doesn't seem to be related to the Categorical/Continuous thing...</span><br /><br />Message: For input string: &quot;MUT&quot;<br /><br />-------------------------------------------------------------<br />java.lang.NumberFormatException: For input string: &quot;MUT&quot;<br />&nbsp;&nbsp;&nbsp; at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)<br />&nbsp;&nbsp;&nbsp; at java.lang.Float.parseFloat(Unknown Source)....<br /><br /><span style="font-weight: bold;">Found/requested 3/22 (with installed Gsea2):</span><br /><br />Run GSEA, add a phenotypes file, create phenotypes on the fly (works fine), click the Show Phenotypes from all Sources. Should show labels from both the file you added and the one you just created, but now shows only one at a time. (This seems to have broken in the 3/21 build; I'm pretty sure it was working in the 3/20 build).<br /><span style="color: rgb(255, 0, 255);">Open&nbsp; (4/24) </span><br /></p>
<p><span style="font-weight: bold;">Beta testing 4/18:</span><br />1. Created a tiny dataset with 4 samples; create phenotype on the fly with 1 sample in ClassA and 3 in ClassB; got this error. If I create phenotype on the fly with 2 samples in each class, life is good.<br /><br />Nan hit score for feature: TACC2 ---- Stack Trace ---- # of exceptions: 1 ------Nan hit score for feature: TACC2------ java.lang.IllegalStateException: Nan hit score for feature: TACC2 at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore_all_modes(KSCore.java:137) at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore(KSCore.java:46) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:377) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:292) at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156) at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130) at xtools.gsea.Gsea.execute_one(Gsea.java:152) at xtools.gsea.Gsea.execute(Gsea.java:104) at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:464) at java.lang.Thread.run(Unknown Source) 2. From the command line, gene set names have to be case sensitive. They should be case INsensitive. (Tested using xtools.gsea.LeadingEdgeTool, where -gsets is comma-separated list of gene set names.)<br /><br /><span style="color: rgb(255, 102, 0);">If 2 samples or less in a class then signal to noise, tTest will not work. Need to use ratio of means.</span><br /><span style="color: rgb(255, 0, 255);">If you want to trap the error and provide a &quot;standard&quot; error box with a help button; I'm happy to write wiki text for it. </span><br /><br /><span style="font-weight: bold;">Found 4/4:</span><br /><br />1. Specify Bhattacharyya with Continous pheno, should get error 1011 (get hardcoded error). Metric for ranking genes parameter.<br /><br /><span style="color: rgb(255, 102, 0);">Bhattacharyya is a continuous metric so isnt this correct?</span><br /><span style="color: rgb(255, 0, 0);">When I run Bhattacharyya with a continuous phenotype I get the following error (no error help button):</span><br /><br />&nbsp;Tool execution error<br />&nbsp;Message: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50<br />&nbsp;This metric can only be used with 2 class comparisons<br /><br />-------------------------------------------------------------<br />java.lang.RuntimeException: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50<br />&nbsp;This metric can only be used with 2 class comparisons<br />&nbsp;&nbsp;&nbsp; at edu.mit.broad.genome.alg.VectorSplitter._barf_not_biphasic(VectorSplitter.java:71)....<br /><br />2. Specify Pearson with Categorical, should get error 1010 (get hardcoded error). Metric for ranking genes parameter.<br /><br /><span style="color: rgb(255, 102, 0);">Pearson is allowed for categorical &amp; continuous</span><br /><span style="color: rgb(255, 0, 0);">When I run Pearson with a Categorical phenotype, I get the following error (no help button); now that I look more closely, it doesn't seem to be related to the Categorical/Continuous thing...</span><br /><br />Message: For input string: &quot;MUT&quot;<br /><br />-------------------------------------------------------------<br />java.lang.NumberFormatException: For input string: &quot;MUT&quot;<br />&nbsp;&nbsp;&nbsp; at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)<br />&nbsp;&nbsp;&nbsp; at java.lang.Float.parseFloat(Unknown Source)....<br /><br /><span style="font-weight: bold;">Found/requested 3/22 (with installed Gsea2):</span><br /><br />Run GSEA, add a phenotypes file, create phenotypes on the fly (works fine), click the Show Phenotypes from all Sources. Should show labels from both the file you added and the one you just created, but now shows only one at a time. (This seems to have broken in the 3/21 build; I'm pretty sure it was working in the 3/20 build).<br /><span style="color: rgb(255, 0, 255);">Open&nbsp; (4/24) </span><br /></p>

Revision as of 16:28, 24 April 2006

Notes

1. By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag.

2. Rejected/Revised bugs removed from this page: see GSEA_enh_history.doc.

Enhancements/Bugs

Beta testing 4/18:
1. Created a tiny dataset with 4 samples; create phenotype on the fly with 1 sample in ClassA and 3 in ClassB; got this error. If I create phenotype on the fly with 2 samples in each class, life is good.

Nan hit score for feature: TACC2 ---- Stack Trace ---- # of exceptions: 1 ------Nan hit score for feature: TACC2------ java.lang.IllegalStateException: Nan hit score for feature: TACC2 at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore_all_modes(KSCore.java:137) at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore(KSCore.java:46) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:377) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:292) at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156) at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130) at xtools.gsea.Gsea.execute_one(Gsea.java:152) at xtools.gsea.Gsea.execute(Gsea.java:104) at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:464) at java.lang.Thread.run(Unknown Source) 2. From the command line, gene set names have to be case sensitive. They should be case INsensitive. (Tested using xtools.gsea.LeadingEdgeTool, where -gsets is comma-separated list of gene set names.)

If 2 samples or less in a class then signal to noise, tTest will not work. Need to use ratio of means.
If you want to trap the error and provide a "standard" error box with a help button; I'm happy to write wiki text for it.

Found 4/4:

1. Specify Bhattacharyya with Continous pheno, should get error 1011 (get hardcoded error). Metric for ranking genes parameter.

Bhattacharyya is a continuous metric so isnt this correct?
When I run Bhattacharyya with a continuous phenotype I get the following error (no error help button):

 Tool execution error
 Message: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50
 This metric can only be used with 2 class comparisons

-------------------------------------------------------------
java.lang.RuntimeException: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50
 This metric can only be used with 2 class comparisons
    at edu.mit.broad.genome.alg.VectorSplitter._barf_not_biphasic(VectorSplitter.java:71)....

2. Specify Pearson with Categorical, should get error 1010 (get hardcoded error). Metric for ranking genes parameter.

Pearson is allowed for categorical & continuous
When I run Pearson with a Categorical phenotype, I get the following error (no help button); now that I look more closely, it doesn't seem to be related to the Categorical/Continuous thing...

Message: For input string: "MUT"

-------------------------------------------------------------
java.lang.NumberFormatException: For input string: "MUT"
    at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
    at java.lang.Float.parseFloat(Unknown Source)....

Found/requested 3/22 (with installed Gsea2):

Run GSEA, add a phenotypes file, create phenotypes on the fly (works fine), click the Show Phenotypes from all Sources. Should show labels from both the file you added and the one you just created, but now shows only one at a time. (This seems to have broken in the 3/21 build; I'm pretty sure it was working in the 3/20 build).
Open  (4/24)

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