Deseq2 Padj = NA

Question

[Cicciongs]

Hello, this is the first time that I write here, I need help with my data. I have performed an RNA-seq with 2 controls and 2 treats. I have after NOIseq filtering 17554 genes but when I do contrast with Deseq2 and filter out all padj = NA only 5983 genes remain, among this only 8 have a padj < 0.05.

Do you know why I have too many genes with a padj = NA?

Thanks a lot.

Answer 1

[rpolicastro]

DESeq2 has a section in their documentation that states why adjusted p-values will be set to NA. The reasons include genes with outlier counts, having low mean expression values, and having all 0 counts. Without seeing your data and code it would impossible to give any specific advice unfortunately.

[Cicciongs]

Thank you. I have see DESeq2 documentation and I think that the reason is :

"If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA. Description and customization of independent filtering is described below"

because I have a pvalue and only the padj is NA. I will check better this situation.

Thanks you very much

[Michael]

You can turn independent filtering off, then the result should be the same as running p.adjust on the raw p-values.

[cortiz]

Hi rpolicastro, Did you manage to know the reason for obtaining adj. pvalue NA after performing DESEQ2?