How to calculate P-value&FDR

[lynn012]

Hi,
When I analyse the significance of gene expression profiles, I should calculate the P-value&FDR. But I don't know how to calculate.Grateful for answers.
Thanks!

[dariober]

Hi,
When I analyse the significance of gene expression profiles, I should calculate the P-value&FDR. But I don't know how to calculate.Grateful for answers.
Thanks!

Hi,

If you are talking about a microarray experiment have a look at the R/Bioconductor package limma. If it is next gen data (RNAseq, Chipseq) see the packages edger or deseq. If instead you want to convert a vector of p-values to fdr values see the function p.adjust in R.

(A suggestion... I think you should make your questions a bit more detailed for people to help!)

Dario

[lynn012]

Dario,
Thanks for your help and I will make my questions a bit more detailed in the future. My data is next gen data(DGE). Thanks for your timely answer and patient explaination again!