Question

Pvalue equals 0 in DESeq2 & fixing for volcano plot

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algejohnson • 0

@algejohnson-20362

Last seen 5.6 years ago

Hi All,

I am having a bit of trouble interpreting a result after running DESeq2 on an RNA-seq dataset with 6 biological replicates for multiple conditions (comparing a parental cell line and multiple independent gene KOs). In particular, for a couple genes I am observing Pvalues of 0, which I interpret as them being even smaller than the closest numeric Pvalue listed of "2.18E-269" (I know, incredibly small). I have independent validation that these genes with Pvalues of 0 are real changes, so it seems logical that I'd be able to plot them in a traditional volcano plot after -log10 transformations, but this transformation obviously doesn't work when the Pvalue=0.

I have seen similar topics discussed in other forums, but haven't seen an exact solution to this problem. Should I re-run the analysis with different parameters so that I have more believable Pvalues? Or should I be imputing values in place of the 0?

Thanks, Alex

deseq2 • 4.4k views

ADD COMMENT • link updated 5.6 years ago by Michael Love 42k • written 5.6 years ago by algejohnson • 0

score 1 · Answer 1 · 2019-03-30

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Michael Love 42k

@mikelove

Last seen 11 hours ago

United States

I don’t really see this as an issue, you can put some arbitrary small pvalue that’s less than alll other pvalues for plotting. I’m only concerned with forming FDR sets, and genes with counts that lead to trivial rejection of the null and have minuscule pvalues will make it into such sets.

ADD COMMENT • link 5.6 years ago Michael Love 42k

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Indeed, that is what I do in EnhancedVolcano. I set these to the machine-specific lowest value with:

 if (min(toptable[,y], na.rm=TRUE) == 0) {
    warning(paste("One or more P values is 0.",
      "Converting to minimum possible value..."),
      call. = FALSE)
    toptable[which(toptable[,y] == 0), y] <- .Machine$double.xmin
  }

ADD REPLY • link 5.6 years ago Kevin Blighe ★ 4.0k

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Great! Many thanks for the quick response and useful advice Michael and Kevin. I think this should solve my problem and I'll try out the method in EnhancedVolcano.

Alex

ADD REPLY • link 5.6 years ago algejohnson • 0