>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