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6.8 years ago

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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 ?

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...

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

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?

There are a couple reasons that one can get an

`NA`

adjusted p-value in DESeq2, the most common of which is due to independent filtering. I will quote from`help(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.

What do you mean by 'no p-value at all'. There must be some value like 'NA' or ''NaN' ...

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