I have analysed gene expression microarray results using limma and have a list of pvalues. I want to use qvalue to look for the FDR. Every time I try to use qvalue I get the error : "ERROR: The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda."
I have repeated my limma analysis and end up with the same results. The p values look OK to me and are all within the range 0-1. My working is as below:
> setwd("~/Desktop/mRNA arrays/")
 0.000299344 0.753304443
> qobj<- qvalue(p=pvalues)
Error in pi0est(p, ...) :
ERROR: The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda.
Could anyone please explain why I am getting this message?
Clinical Research Fellow
University of Birmingham, UK