[BioC] flat microarray p-values

Darren Ames ames at Ag.arizona.edu
Thu Jun 1 21:02:11 CEST 2006

Hi Sean,

Thanks for the reply. Upon closer inspection of the data, it appears that
the qvalue package is working, but the output is just wonky. I get numbers
that are the same value near 1 for all genes for most of my comparisons. The
B-statistic is also a negative value. Could there be something in the gpr
file that is causing this to occur?


-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: Thursday, June 01, 2006 4:01 AM
To: Darren Ames
Subject: Re: [BioC] flat microarray p-values

On 5/31/06 6:23 PM, "Darren Ames" <ames at Ag.arizona.edu> wrote:

> I have a problem with my latest batch of microarrays. A histogram of all
> p-values is flat, so the qvalue package does not work. Quality control
> indicates that these are good arrays. Does anyone have any ideas?

What doesn't work about the qvalue package?  (I don't use it much, so I may
not be helpful, but....)  What commands have you tried and what is the


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