transcript length bias in enrichment analysis and RPKM

PFS · 12-10-2010, 01:41 PM

I read about the need of correcting for transcript length bias when performing GO enrichment analysis in RNA-Seq data.

If we use RPKM values instead of raw counts, is this still true?

frozenlyse · 12-12-2010, 06:32 PM

No - check out this reference which goes through the reasoning and tries to address the problem though http://genomebiology.com/content/11/2/R14

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12-10-2010, 01:41 PM	#1
PFS Member Location: USA Join Date: Mar 2010 Posts: 55	transcript length bias in enrichment analysis and RPKM I read about the need of correcting for transcript length bias when performing GO enrichment analysis in RNA-Seq data. If we use RPKM values instead of raw counts, is this still true?

12-12-2010, 06:32 PM	#2
frozenlyse Senior Member Location: Australia Join Date: Sep 2008 Posts: 136	No - check out this reference which goes through the reasoning and tries to address the problem though http://genomebiology.com/content/11/2/R14