3 Control replicate and 2 test sample ,so Im comparing my Control which is my Progenitor cells to Monocyte which is mature stage

this is my code im using

condition <- factor(c(rep("Control", 3),rep("Test", 2)),levels=c("Control", "Test"))

(coldata <- data.frame(row.names=colnames(countdata), condition))
dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)

This is my deseq2 output

gene baseMean log2FoldChange lfcSE  stat pvalue padj CB1 CB2 CB3 GD5_1  GD5_2
ENSG00000144655 2030.6146124999 -5.0812043868   0.1183868766    -42.9203348727  0   0   3327.4890036209 3267.1877800456 3362.7407570783 98.5079578403   97.1475639145

Im not sure how come the pvalue and padj is 0? even though the sample value there is a difference and there is also fold change ,something wrong with the result ?

  • 1
    $\begingroup$ What's your sample design? How many biological reps do you have? $\endgroup$ Apr 18, 2018 at 10:48
  • $\begingroup$ I have updated it $\endgroup$
    – kcm
    Apr 18, 2018 at 11:00

1 Answer 1


A p-value of 0 is expected in this case. The p-values are calculated by comparing the Wald stat to a standard normal, so you can confirm that this is correct like this:

> pnorm(-42.9203348727)
[1] 0

It really means p < 2.225074e-308 See here for a more details

  • $\begingroup$ Yes i checked the post it has similar issue ,but pardon my ignorance but how come the deseq2 normalised value are so large CB1 CB2 CB3 GD5_1 GD5_2 3327.4890036209 3267.1877800456 3362.7407570783 98.5079578403 97.1475639145 yet these are not significant? can you explain me in simpler manner and relate with the biology , you can expand your current answer ..thank you in advance $\endgroup$
    – kcm
    Apr 18, 2018 at 11:13
  • 2
    $\begingroup$ small p-values are more significant, so a p-values less than 2.3e-308 is very, very significant. It's as significant as you can get $\endgroup$ Apr 18, 2018 at 11:34

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.