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Old 08-21-2012, 09:46 AM   #1
proteomania
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Default DESeq and GSEA with pre-ranked gene list

Hi all,

I've been using DESeq for my RNA-Seq differential expression analysis. Now I want to use the DESeq result to generate a ranked-list, which will be used as the input in GSEA. My question is: Should I rank the genes using the fold changes or using the q-values?

Thanks.
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Old 08-21-2012, 11:50 PM   #2
Simon Anders
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How to combine GSEA with RNA-Seq is still unclear and subject to ongoing research. We (and other groups, I suppose) are looking at a couple of options.

If you want something now, try using the moderate log fold change that are now reported by the newest version of DESeq. This is not ideal, and I don't want to even say that it is statistically sound, but it is probably better than using p values or raw fold changes.
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Old 07-28-2013, 11:20 AM   #3
hlestrella
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Default DESeq and GSEA with pre-ranked gene list

Quote:
Originally Posted by Simon Anders View Post
How to combine GSEA with RNA-Seq is still unclear and subject to ongoing research. We (and other groups, I suppose) are looking at a couple of options.
I'm also interested in using RNA-Seq differential expression results as a ranked list into GSEA. Any new thoughts since last August on more appropriately ranking the genes coming out of DE analysis for GSEA (or other gene enrichment analyses)?
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Old 02-18-2014, 12:29 AM   #4
maxUlysse
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Have you looked into SeqGSEA ?
cf : http://bioinformatics.oxfordjournals...tu090.abstract
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Old 02-16-2015, 07:58 PM   #5
apredeus
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Quote:
Originally Posted by Simon Anders View Post
How to combine GSEA with RNA-Seq is still unclear and subject to ongoing research. We (and other groups, I suppose) are looking at a couple of options.

If you want something now, try using the moderate log fold change that are now reported by the newest version of DESeq. This is not ideal, and I don't want to even say that it is statistically sound, but it is probably better than using p values or raw fold changes.
Hello Simon,

since this is such an old post, I figured I'd ask if there were any advances on the issue - either from your group or anybody else?

I've tried few things but I quite come up with a criterion about what's working and what's not. Is using Wald statistic in pre-ranked GSEA a bad idea?

Thank you for any input in advance.
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Old 02-16-2015, 08:02 PM   #6
apredeus
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Quote:
Originally Posted by maxUlysse View Post
Have you looked into SeqGSEA ?
cf : http://bioinformatics.oxfordjournals...tu090.abstract
This is good, but it kind of forces you to use their own differential expression analysis. I would like to stick with DESeq2, and then use the results in GSEA.
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Old 02-17-2015, 02:25 AM   #7
turnersd
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(Old post, but folks are still watching, still high google rank.)
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Old 02-17-2015, 11:08 AM   #8
Michael Love
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I haven't done any testing on what output is best for downstream set analysis. I recently wrote a post on Bioc support site on how to produce a discrete output (yes/no DE) from DESeq2 for use with the Bioc package goseq. Another option would be to use the moderated LFC or Wald statistic as a continuous signal.
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