Hi everyone,
I have done a pair comparison with DEseq to find differentially expressed genes between two samples, for each sample i hvae four replicates, for the DEseq result, i got exactly same padj value for all the genes and it is not significant, is this normal ? I feel it is weird, even if there is no significantly expressed genes, I don't think the padj shoulf be the same for all the genes. Does anyone know what is going on here?
Thank you in advance.
If there is never or little evidence against the null hypothesis the fdr is going to be always close to one, with many values the same. For example:
set.seed(1234)
p<- runif(n= 10000, min= 0, max= 1) ## Random pvalues
padj<- p.adjust(p, method= 'fdr')
unique(padj) ## Only 63 instead of 10000!
[1] 0.9933484 0.9952445 0.9523590 0.9934287 0.9973141 0.9950672 0.9850355
[8] 0.9935054 0.9983892 0.9955913 0.9975077 0.9985928 0.9956708 0.9992315
[15] 0.9981005 0.9943607 0.9894110 0.9979089 0.9945797 0.9977378 0.9960884
[22] 0.9971430 0.9919923 0.9920665 0.9963164 0.9943261 0.9952540 0.9994030
[29] 0.9939164 0.9950848 0.9948379 0.9991311 0.9950674 0.9990905 0.9956615
[36] 0.9856121 0.9953103 0.9936643 0.9966662 0.9968053 0.9948980 0.9947535
[43] 0.9981661 0.9981403 0.9943537 0.9992011 0.9943544 0.9574976 0.9984791
[50] 0.9987469 0.9934477 0.9995938 0.9865497 0.9954706 0.9989503 0.9936114
[57] 0.9990756 0.9993953 0.9943536 0.9915178 0.9913084 0.9806490 0.9984822
Hi,
Here is my response to this question on the Bioconductor mailing list: https://support.bioconductor.org/p/51916/#51952
Essentially, the same padj value repeated for multiple genes is a normal consequence of the Benjamini and Hochberg adjustment.
•
written
by
Michael Love
gene padj
a 0.999909
s 0.999909
d 0.999909
f 0.999909
g 0.999909
h 0.999909
j 0.999909
n 0.999909
b 0.999909
m 0.999909
n 0.999909
c 0.999909
z 0.999909
x 0.999909
Thousands of genes got the same padj (0.999909). It is almost eaqual to 1. So this is normal? Thank you very much.
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I am curious that what fold changes value you are getting for these genes?
Are they also close to one?