I was playing around with weights and examining the results. I changed the wieghts prior to doing duplicateCorrelation,lmFit,eBayes and topTable in limma. Changing all weights to 1 (were previously they were 1 or 0) had a dramatic affect on M values, but did nothing to A. Is this intended? I would think that if you flagged something, you would not want the results included in the calculations for A. -Lance Palmer [[alternative HTML version deleted]]

On May 18, 2005, at 4:18 PM, lepalmer@notes.cc.sunysb.edu wrote: > I was playing around with weights and examining the results. I > changed > the wieghts prior to doing duplicateCorrelation,lmFit,eBayes and > topTable > in limma. Changing all weights to 1 (were previously they were 1 or 0) > had a dramatic affect on M values, but did nothing to A. Is this > intended? I would think that if you flagged something, you would not > want > the results included in the calculations for A. The A values do not enter calculations of duplicateCorrelation, lmFit, eBayes, or topTable, as far as I know. They are reported in topTable, yes, but A values don't affect which genes show up as differentially expressed. Is there a specific reason you want to know the "weighted" A-values--just curious? Sean

Additionally to Seans comments, the row mean of the A matrix is all that is calculated in lmFit as if (length(object@maA)) fit$Amean <- rowMeans(unwrapdups(object@maA, ndups = ndups, spacing = spacing), na.rm = TRUE) } which are not weighted, and the Amean is reported in topTable (if it in the list). In plotMA(fit) you will have some small differences in the Amean's xcoordinate compared to using a weighted mean to calculate A values when highlighting genes predicted to be differentially expressing. Marcus >>> Sean Davis <sdavis2@mail.nih.gov> 18/05/2005 11:20:05 p.m. >>> On May 18, 2005, at 4:18 PM, lepalmer@notes.cc.sunysb.edu wrote: > I was playing around with weights and examining the results. I > changed > the wieghts prior to doing duplicateCorrelation,lmFit,eBayes and > topTable > in limma. Changing all weights to 1 (were previously they were 1 or 0) > had a dramatic affect on M values, but did nothing to A. Is this > intended? I would think that if you flagged something, you would not > want > the results included in the calculations for A. The A values do not enter calculations of duplicateCorrelation, lmFit, eBayes, or topTable, as far as I know. They are reported in topTable, yes, but A values don't affect which genes show up as differentially expressed. Is there a specific reason you want to know the "weighted" A-values--just curious? Sean _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}