RNA-Seq analysis with standard p-value
I have analyzed RNA-Seq data using standard thresholds of logFC 2 and p-vlaue 0,05 using Deseq2 package. I am expecting one particular candidate gene which I have found from qPCR. In RNA-Seq resutls when I look for that gene logFC is 4 and padjval is 0,00. I am not able to understand why so ?
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What's unexpected about that finding? padjval indicates very significant, logFC is reasonably big.
In simple way..as p-value is 0 its not in my candidate gene list because of which I have to exclude it. Were as I expect it to be in the candidate gene list. So, I am trying to find out reason/s of p-value being 0.Yes logFC is higher.
Pvalue = 0 means too significant to represent by a tiny number. So it's very significant. And smaller than 0.05. So it's differentially expressed. Why would you exclude it then?
What p-value threshold are you using where 0 is not less than it?
Using p-value 0.05. I didnt get you what you mean?
So
therefore this gene is significant and should not be excluded
I think why you are confused is because you do not see the (-) sign at your padjval column. That (-) sign you are not seeing is there to show you 10's power. so when its -5, it is 10^-5, which is a small number between 1 and 0. when padj is 0, it is the highest significance value that you can get, so there is no confusion in your results. spend a bit more time on understanding and interpreting results rather than simply filtering them.
The adjusted p-value column isn't log10 transformed...
Thanks all for the reply I understand p=0 is highly significant.
now another case of gene where there is no p-value at all, not even zero , what does this says?
What do you mean by 'no p-value at all'. There must be some value like 'NA' or ''NaN' ...
There are a couple reasons that one can get an
NAadjusted p-value in DESeq2, the most common of which is due to independent filtering. I will quote fromhelp(results):Thanks for this information Devon , I have exactly followed the same thing from Deseq2 vignette and have disable the independent filtering and cooksCutoff both to avoid default filtering of such candidate genes and it worked fine.
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