p-value "NA" in DESeq eventhough counts across the replicates and conditions is not zero
Hi,
I am getting p-value as "NA" eventhough the log2FC is greater than 6 for the following three transcripts. Can somebody explain me if you have across this anytime?
"id","baseMean","baseMeanA","baseMeanB","foldChange","log2FoldChange","pval","padj"
"ENST00000464588",21567.0703963241,367.539692089608,42766.6011005586,116.359136226658,6.86244068175062,NA,NA
"ENST00000526359",13369.6103749259,109.604047639007,26629.6167022127,242.961982480066,7.92458677529959,NA,NA
"ENST00000532801",12831.1517683669,393.734085139833,25268.569451594,64.1767385788302,6.00397856952259,NA,NA
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are you using DESeq or DESeq2?
I am using DESeq.
This would make more sense if you were using DESeq2, since then these could be genes with apparent outliers. I don't recall there being any mechanism for this in DESeq.
Regardless, you should really be using DESeq2 anyway (it has a good number of improvements).
Im tried DESeq2 for the same data and this time it is the different set transcripts which are showing "NA" as their p-value
The 3 transcripts, where p-value was "NA" for DESeq are showing p-value as 0 with DESeq2
I'd go with the DESeq2 results. There are known reasons, described in the user manual, why it will sometimes yield NA p-values.