Entering edit mode
Dear all,
Has anyone an idea why some of my results from a DESEQ2 analysis have empty pvalue and padj value. Most of the genes have a pvalue and padj but for some genes for a reason I dont understand they are completely empty. In case the value is 0 for other genes it would show a "0". So empty seems not to be equal to zero.
Example:
| log2FoldChange | pvalue | padj |
|---|---|---|
| 2 | ||
| 2 | ||
| 1 | 2.03843E-05 | 0.023951556 |
| 1 | 0.00070128 | 0 |
Line 1 and 2 have no pvalue and no padj.
Thank you for any ideas!
Bine
Okay thanks for clarifying. Actually I just realized that it shows NA in R but then when printing to Excel it gets empty. This I can fix.
But still dont understand then why some values it has NA ?
Read the manual, unsurprisingly it is covered there: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na
It is very unlikely that you will stumble over an issue that cannot be solved by reading the manual, or browsing this community (e.g. via google where it is indexed or the in-built search function), or searching biostars.org for it. Most (if not all) standard issues have been asked before given the heavy use of DESeq2 across the bioinformatics community. Please put in some effort.