RNASEQ GE analysis, p-values zero whereas fold changes are not??

Question

[begumozemek]

Hi all, I am quite new around here, so if it was asked sorry for creating a duplicated post, but I could not find it. I have TCGA data downloaded and trying to analyze differentially expressed genes by using edgeR.

in BRCA, two of genes have p-values and FDR zero (I don't know if it is an underflow or literally zero) and fold changes around -3,5 and -2,4. I don't know how to interpret these extremely low p-values. Are they because of a biological variation or a statistical error? Maybe I should have made some kind of normalization? Additionally, my p-values of other genes are extremely low, too (around e-305) and for other cancers I found p-values around e-60. So maybe, I am missing something.

Thanks!

edit: I am working with patient tumor/normal tissue pairs.

[spvensko]

https://support.bioconductor.org/p/64787/#64792 seems to answer your question.

[begumozemek]

Thanks for your interest, however my common dispersion value is 0,6 for this type of cancer and it is consistent with other types (they are also around 0,57-0,6). I observed these radical p-values only in BRCA.

[Satyajeet Khare]

Small p-values indicate significant change. Fold change (assuming log2) of -3.5 or 2.4 indicates decrease in expression of genes. So the genes of your interest are significantly downregulated.

[begumozemek]

Thanks for clarification, I just found strange these extremely low p-values.

[WouterDeCoster]

Yes but p-values far smaller than reasonable are a reason to be suspicious.