Difference between revisions of "Gsea enhancements"
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| − | As the software is almost perfect, there are few bugs and little need for enhancements.<br /><br /><span style="font-weight: bold;">Found/requested 3/22 (with installed Gsea2):<br /></span><br />1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected.<span style="font-weight: bold;"><span style="font-weight: bold;"> </span></span>But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.<br /><br />2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)<br /><br />3. On Leading Edget report, when I click select reports from application cache, I expected to get today's reports (the ones in the Object Cache list on the Load Data page). Instead, I get a list of all reports, neatly arranged by date, excluding todays. When I run reports, they appear in the Object Cache as I expect.<br /><br />4. Run GSEA using the new Gene Matrix from web site tab to select the C2 gene sets. Analysis fails due to duplicate gene sets.<span style="font-weight: bold;"><span style="font-weight: bold;"><br /><br /></span></span>5. On the new error handling, when I click the red error in the processes box, it should automatically open the console viewer and show me the error. It took me a litle bit to realize that I had to Click for details... to open the console and then click Error to see the error.<br /><br />6. Analysis History page still isn't showing up for me. <br /><br />7. On MSigDB page, when I click export, I'm expecting to export what I have displayed in the table on the MSigDB page. When I selected All Items, I thought that meant all items displayed in the table; it seems mean all items in the MSigDB? (thanks for going back to one button)<br /><span style="font-weight: bold;"><span style="font-weight: bold;"><br />Feature Additions for build 3/2</span>1<br /><br /></span>1. Leading edge interactive viewer<br />2. Added a preferences field for path to user home dir.<br />3. made native the default space in gsea. Not sure if this is better??<br /> <span style="color: rgb(0, 0, 255);"> I prefer gene_symbol since that's what we recommend.</span><br />4. default collection of gene sets available via ftp<span style="font-weight: bold;"><br /><br /><span style="font-weight: bold;">Found/requested 3/17:</span><br /><br /></span>1. Add Command button to Leading Edge page.<br /><br /><span style="color: rgb(255, 0, 0);">Cant do this easilly because of the way the command thing is setup.<br /><span style="color: rgb(0, 0, 255);">You said you could do this after all.</span><br /></span><br />2. Leading edge from command line give me fatal errors:<br /> 719 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases at <br /> edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)<br /> 719 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip at <br /> edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)<br /> 799 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo at<br /> edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)<br /><br />Must set -DGSEA=true flag<br />So,<br /><br /> <pre>java -Xmx ... -DGSEA=true xtools.....</pre> <br /><br />3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the<br /> Find sets that contain this gene page.<br /><br /><span style="color: rgb(255, 153, 0);">Joshs reworked impl will replace this and the export option should be added to it</span><br /><br />4. On Run GSEA, change parameter name from "Analyze in the feature space" to "Gene/probe identifier format"<br /><br /><span style="color: rgb(255, 0, 0);">Lets talk. <span style="color: rgb(0, 0, 255);">Forgot to bring this up in our last chat.</span></span><br /><br />5. Remove Downloads>Download Gene Sets (no longer needed now that we have MSigDB page).<br /><br /><span style="color: rgb(51, 153, 102);">Done</span><br /><br />6. Change first two Help items to "GSEA web site" and "GSEA documentation". First points to home page of web site and<br /> second points to the doc page of the web site.<br /><br /><span style="color: rgb(51, 153, 102);">Done</span><br /><span style="font-weight: bold;"><br /><span style="font-weight: bold;">Bugs found 3/15/2006 include:</span><br /><br /></span>1. Generate a report, go to "Other" section, look at parameters. Error, file cannot be found.<br /><br />Fixed.<br /><br />2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.<br /><br />Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)<br /><br />3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.<br /><br />Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen. | + | As the software is almost perfect, there are few bugs and little need for enhancements.<br /><br /><span style="font-weight: bold;">Found/requested 3/22 (with installed Gsea2):<br /></span><br />1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected.<span style="font-weight: bold;"><span style="font-weight: bold;"> </span></span>But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.<br /><br />2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)<br /><br />3. On Leading Edget report, when I click select reports from application cache, I expected to get today's reports (the ones in the Object Cache list on the Load Data page). Instead, I get a list of all reports, neatly arranged by date, excluding todays. When I run reports, they appear in the Object Cache as I expect.<br /><br />4. Run GSEA using the new Gene Matrix from web site tab to select the C2 gene sets. Analysis fails due to duplicate gene sets.<span style="font-weight: bold;"><span style="font-weight: bold;"><br /><br /></span></span>5. On the new error handling, when I click the red error in the processes box, it should automatically open the console viewer and show me the error. It took me a litle bit to realize that I had to Click for details... to open the console and then click Error to see the error.<br /><br />6. Analysis History page still isn't showing up for me. <br /><br />7. On MSigDB page, when I click export, I'm expecting to export what I have displayed in the table on the MSigDB page. When I selected All Items, I thought that meant all items displayed in the table; it seems mean all items in the MSigDB? (thanks for going back to one button)<br /><br />8. RunGSEA form, the normalization parameter, you were going to delete the varmean option (or at least change the current name VarMeanPosNegSeparate back to varmean).<br /><span style="font-weight: bold;"><span style="font-weight: bold;"><br />Feature Additions for build 3/2</span>1<br /><br /></span>1. Leading edge interactive viewer<br />2. Added a preferences field for path to user home dir.<br />3. made native the default space in gsea. Not sure if this is better??<br /> <span style="color: rgb(0, 0, 255);"> I prefer gene_symbol since that's what we recommend.</span><br />4. default collection of gene sets available via ftp<span style="font-weight: bold;"><br /><br /><span style="font-weight: bold;">Found/requested 3/17:</span><br /><br /></span>1. Add Command button to Leading Edge page.<br /><br /><span style="color: rgb(255, 0, 0);">Cant do this easilly because of the way the command thing is setup.<br /><span style="color: rgb(0, 0, 255);">You said you could do this after all.</span><br /></span><br />2. Leading edge from command line give me fatal errors:<br /> 719 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases at <br /> edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)<br /> 719 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip at <br /> edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)<br /> 799 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo at<br /> edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)<br /><br />Must set -DGSEA=true flag<br />So,<br /><br /> <pre>java -Xmx ... -DGSEA=true xtools.....</pre> <br /><br />3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the<br /> Find sets that contain this gene page.<br /><br /><span style="color: rgb(255, 153, 0);">Joshs reworked impl will replace this and the export option should be added to it</span><br /><br />4. On Run GSEA, change parameter name from "Analyze in the feature space" to "Gene/probe identifier format"<br /><br /><span style="color: rgb(255, 0, 0);">Lets talk. <span style="color: rgb(0, 0, 255);">Forgot to bring this up in our last chat.</span></span><br /><br />5. Remove Downloads>Download Gene Sets (no longer needed now that we have MSigDB page).<br /><br /><span style="color: rgb(51, 153, 102);">Done</span><br /><br />6. Change first two Help items to "GSEA web site" and "GSEA documentation". First points to home page of web site and<br /> second points to the doc page of the web site.<br /><br /><span style="color: rgb(51, 153, 102);">Done</span><br /><span style="font-weight: bold;"><br /><span style="font-weight: bold;">Bugs found 3/15/2006 include:</span><br /><br /></span>1. Generate a report, go to "Other" section, look at parameters. Error, file cannot be found.<br /><br />Fixed.<br /><br />2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.<br /><br />Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)<br /><br />3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.<br /><br />Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen. |
Revision as of 10:08, 22 March 2006
As the software is almost perfect, there are few bugs and little need for enhancements.
Found/requested 3/22 (with installed Gsea2):
1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected. But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.
2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)
3. On Leading Edget report, when I click select reports from application cache, I expected to get today's reports (the ones in the Object Cache list on the Load Data page). Instead, I get a list of all reports, neatly arranged by date, excluding todays. When I run reports, they appear in the Object Cache as I expect.
4. Run GSEA using the new Gene Matrix from web site tab to select the C2 gene sets. Analysis fails due to duplicate gene sets.
5. On the new error handling, when I click the red error in the processes box, it should automatically open the console viewer and show me the error. It took me a litle bit to realize that I had to Click for details... to open the console and then click Error to see the error.
6. Analysis History page still isn't showing up for me.
7. On MSigDB page, when I click export, I'm expecting to export what I have displayed in the table on the MSigDB page. When I selected All Items, I thought that meant all items displayed in the table; it seems mean all items in the MSigDB? (thanks for going back to one button)
8. RunGSEA form, the normalization parameter, you were going to delete the varmean option (or at least change the current name VarMeanPosNegSeparate back to varmean).
Feature Additions for build 3/21
1. Leading edge interactive viewer
2. Added a preferences field for path to user home dir.
3. made native the default space in gsea. Not sure if this is better??
I prefer gene_symbol since that's what we recommend.
4. default collection of gene sets available via ftp
Found/requested 3/17:
1. Add Command button to Leading Edge page.
Cant do this easilly because of the way the command thing is setup.
You said you could do this after all.
2. Leading edge from command line give me fatal errors:
719 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases at
edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)
719 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip at
edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)
799 [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo at
edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)
Must set -DGSEA=true flag
So,
java -Xmx ... -DGSEA=true xtools.....
3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the
Find sets that contain this gene page.
Joshs reworked impl will replace this and the export option should be added to it
4. On Run GSEA, change parameter name from "Analyze in the feature space" to "Gene/probe identifier format"
Lets talk. Forgot to bring this up in our last chat.
5. Remove Downloads>Download Gene Sets (no longer needed now that we have MSigDB page).
Done
6. Change first two Help items to "GSEA web site" and "GSEA documentation". First points to home page of web site and
second points to the doc page of the web site.
Done
Bugs found 3/15/2006 include:
1. Generate a report, go to "Other" section, look at parameters. Error, file cannot be found.
Fixed.
2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.
Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)
3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.
Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen.
