[BioC] Limma: A values in topTable

[Gordon Smyth]

>Date: Tue, 12 Jul 2005 12:53:32 -0700
>From: "Wu, Xiwei" <XWu at coh.org>
>Subject: [BioC] Limma: A values in topTable
>To: bioconductor at stat.math.ethz.ch
>
>Dear list,
>
>I did a search in the mail achive, and did not find anyone reporting the
>same issue below.
>I was looking at some cDNA array data using Limma 2.0.2 with
>R2.1.1patched under Windows2000. I have three different contrasts. When
>I looked at the topTables generated from each contrasts, the A (average
>intensity) for all the genes are the same across the three contrasts. I
>also observed the same thing using another dataset. Is that what is
>supposed to happen, or is there anything wrong with my code?

Yes, that is supposed to happen. The A-value is the average intensity for 
that probe over all arrays in the experiment, not just over the specific 
set of contrasts.

Gordon

>  Any help
>will be highly appreciated.
>
>Xiwei Wu, MD, PhD
>Assistant Research Scientist
>Department of Biomedical Informatics
>Beckman Research Insitute
>City of Hope National Medical Center
>Duarte, CA 91010