Question: Issues in generating workable rank file for GSEA
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17 months ago by
csijst0
Singapore/National University of Singapore
csijst0 wrote:

Hi,

I'm trying to generate a ranking file for my differential expressed genes that was generated via DESeq2. I saw some websites like Genome Spot that taught me how to use the p-values and log2foldchange to rank the genes. But in DESeq2 output, some of them appear as "NA". And this will reappear in the ranking file. Apparently, pre-ranked GSEA either java Desktop application (from Broad Institute) or GenePattern are not able to process the NA entries.

As such, what should I do for genes that display NA? As in what is the usual procedure in handling such information? Remove them?

Thank you.

modified 17 months ago by Michael Love25k • written 17 months ago by csijst0
Answer: Issues in generating workable rank file for GSEA
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17 months ago by
assaron150
assaron150 wrote:

Hi,

In DESeq2 you can use t-statistic for ranking, there are no NA-s. If you still want to use p-values, set DESeq2 option cooksCutoff=FALSE for the results function.

Hi,

I tried the command,

dDif_res <- results(dLRT, contrast=c("treatment", "shRNA", "ctrl"), alpha=0.05, altHypothesis="greaterAbs", cooksCutoff=FALSE)

But the output still shows NA for some of the genes. These genes do not have any baseMean as well.

Answer: Issues in generating workable rank file for GSEA
0
17 months ago by
Michael Love25k
United States
Michael Love25k wrote:

You can also set NA to 1. There’s example code for this in the vignette FAQ