V2 notes from user testing

From GeneSetEnrichmentAnalysisWiki

(Difference between revisions)
Jump to: navigation, search
(Out of memory error)
 
(3 intermediate revisions not shown)
Line 1: Line 1:
-
<h2>Notes from testing/user feedback of beta v2 software</h2>
+
<p>This page was intended to capture&nbsp; &quot;gotchas&quot; and &quot;confusions&quot; that users encountered in using the V2 software. These observations can now be captured in [http://bugzilla.broad.mit.edu/gsea/ Bugzilla] as documentation and/or software enhancements. </p>
-
<br /><span style="color: rgb(0, 0, 255);">Fill in gotchas, observations of user behavior etc for the v2 software</span><br style="color: rgb(0, 0, 255);" /><br style="color: rgb(0, 0, 255);" /><span style="color: rgb(0, 0, 255);">(dont enter bugs here, use [[Gsea_enhancements]] instead</span><br /><br /><br /><span style="font-weight: bold;">I ran gsea v2 and the results not identical to PNAS published results. Theres a bug!</span><br /><br />Probabaly not<br /><br />1) your results modestly different - FDRS change a bit or the order of top gene sets is a little different<br />This is because the FDR for a small number of sets can be a bit choppy in the tail. So, a small diff (few percent) in FDR is not unusual as the random seed used from run to run is different<br />Additionally, the mapping databases have been updated to reflect the latest releases of NetAffx, Unigene and related chip annotations. These changes might have affected the mapping of gene sets from native ids to gene symbols and also the collapsing of datasets from probe ids to gene symbols. Our internal tests show that these effects are minor but nevertheless could account for small differences in FDR<br /><br />2) The results are hugely different<br />Something is wrong and its most likely your fault.<br /><br /><br /><span style="font-weight: bold;">Whats the relation b/w GSEA and the new stuff (MSigDB Browser, Chip2Chip)</span><br /><br />msigdb, chip2chip etc are <span style="font-weight: bold;">not </span>needed for vanilla gsea. You can run gsea with any gene sets.<br />They help find gene sets and map them b/w platforms.<br /><br />For gsea, simply the 3 steps. No need to do mapping etc. Even collapsing is now built in.<br /><br /><br /><span style="font-weight: bold;">GSEA Java Needs</span><br /><br />Needs 1.4+<br />Preferred to use 1.5<br /><br />So if you launch on a mac and see the error message unsupported class version it means that your mac (or windows) doesnt not have the correct java version.<br />For the mac: http://docs.info.apple.com/article.html?artnum=302412
+
===CLS file problem===
 +
<p>CLS file with four classes which was loadable to GSEA ver1 does not load anymore: </p>
 +
<pre>22 4 1
 +
#WTnd WThf KOnd KOhf WTnd WThf KOhf KOhf WTnd WTnd WTnd WTnd WTnd KOnd KOnd KOnd KOnd KOnd KOnd WThf WThf WThf WThf KOhf KOhf KOhf
 +
</pre>
 +
It loads after changing it to:
 +
<pre>22 2 1
 +
#WT KO
 +
WT WT KO KO WT WT WT WT WT KO KO KO KO KO KO WT WT WT WT KO KO KO
 +
</pre>
 +
<p>[[User:Darked|darked]] 13:29, 21 July 2006 (EDT) </p>
 +
<p>==Java Heap Space error=== </p>
 +
<p>On a 2GB Windows XP workstation with no other than GSEA applications running I am getting: </p>
 +
<p>java.lang.OutOfMemoryError: Java heap space </p>
 +
<p>using all.may_2006.symbols_mapped_to_Mouse430_2.gmt, CLS mentioned above + expression file (derived from 22 CEL files of Mouse430_2 platform), 100 permutations . </p>
 +
<p>1) Can I somehow increase available memory, i.e. by running it on a command line? </p>
 +
<p>2) Any other ideas how to complete the job? </p>
 +
<p>[[User:Darked|darked]] 14:26, 21 July 2006 (EDT)</p>

Current revision as of 18:26, 21 July 2006

This page was intended to capture  "gotchas" and "confusions" that users encountered in using the V2 software. These observations can now be captured in Bugzilla as documentation and/or software enhancements.

CLS file problem

CLS file with four classes which was loadable to GSEA ver1 does not load anymore:

22 4 1
#WTnd WThf KOnd KOhf WTnd WThf KOhf KOhf WTnd WTnd WTnd WTnd WTnd KOnd KOnd KOnd KOnd KOnd KOnd WThf WThf WThf WThf KOhf KOhf KOhf

It loads after changing it to:

22 2 1
#WT KO
WT WT KO KO WT WT WT WT WT KO KO KO KO KO KO WT WT WT WT KO KO KO

darked 13:29, 21 July 2006 (EDT)

==Java Heap Space error===

On a 2GB Windows XP workstation with no other than GSEA applications running I am getting:

java.lang.OutOfMemoryError: Java heap space

using all.may_2006.symbols_mapped_to_Mouse430_2.gmt, CLS mentioned above + expression file (derived from 22 CEL files of Mouse430_2 platform), 100 permutations .

1) Can I somehow increase available memory, i.e. by running it on a command line?

2) Any other ideas how to complete the job?

darked 14:26, 21 July 2006 (EDT)

Personal tools