**0**wrote:

Dear All,

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:

library(qvalue)

> setwd("~/Desktop/mRNA arrays/")

> pvalues=read.table("pvalues.txt")

> range(pvalues)

[1] 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?

Thanks,

Clara Green

Clinical Research Fellow

University of Birmingham, UK

**32k**• written 2.3 years ago by robandclara •

**0**

As James Macdonald has explained, based on the range of p-values that you show, your p-value distribution is questionable. A good place to start would be to read this article and see if your p-value distribution has any of the problems described in it: http://varianceexplained.org/statistics/interpreting-pvalue-histogram/

6.3k