Hello everyone, I am working on a set of affymetrix arrays, and I am interested in obtaining the A and B values in lfc = log(A/B). I wrote several small functions to annotate my topTable outputs, and one of these annotations was the exprs() for each probe, but when comparing the lfc's that topTable output, they are very different than the values that I could calculate with the exprs() values. So I am then lead to believe that the lfc is calculated by expression values that have been adjusted/better estimated by eBayes() and so on. So can I take a lfc, A, M, exprs(), et cetera to get the values that the log fold change is directly calculated from? Sorry if this question has been asked, I have no idea how to describe my problem succinctly. Cheers! Sam McInturf -- output of sessionInfo(): > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.

Hi Sam, On 7/27/12 11:51 AM, Sam McInturf [guest] wrote: > Hello everyone, > I am working on a set of affymetrix arrays, and I am interested in obtaining the A and B values in lfc = log(A/B). > > I wrote several small functions to annotate my topTable outputs, and one of these annotations was the exprs() for each probe, but when comparing the lfc's that topTable output, they are very different than the values that I could calculate with the exprs() values. So I am then lead to believe that the lfc is calculated by expression values that have been adjusted/better estimated by eBayes() and so on. Your functions must be wrong. If by lfc you mean logFC, or more accurately log fold change (being precise with your language always helps - when people have to infer what you mean then you may well not get your question answered to your satisfaction), then there is no adjustment to this quantity by the empirical Bayes step. Please note here that the empirical Bayes step has to do with adjustments made to the denominator of your t-statistic, which estimates the intra-group variability, rather than the numerator which estimates the log fold change between two samples. There is no adjustment made to the numerator. Here is an example you can try: > set.seed(0xabeef) ## for reproducibility, so you get the exact same results > mat <- matrix(rnorm(10000), ncol=10) > design <- model.matrix(~factor(rep(1:2, each=5))) > fit <- lmFit(mat, design) > fit2 <- eBayes(fit) > topTable(fit2, 2) logFC t P.Value adj.P.Val B 541 -2.253898 -3.571210 0.0003773231 0.3773231 -0.9993917 398 2.052834 3.238471 0.0012530516 0.5878160 -1.7256870 335 -1.947496 -3.096086 0.0020317486 0.5878160 -2.0155870 928 1.905416 3.027252 0.0025498760 0.5878160 -2.1512171 556 -1.882673 -2.983539 0.0029390799 0.5878160 -2.2358166 506 1.788323 2.845245 0.0045551320 0.7248347 -2.4955945 874 1.774333 2.810355 0.0050738428 0.7248347 -2.5592404 635 -1.687085 -2.681715 0.0074808935 0.7883527 -2.7872997 257 -1.680194 -2.666920 0.0078151322 0.7883527 -2.8128618 461 1.668451 2.654302 0.0081107165 0.7883527 -2.8345537 Note here that the top fake gene is in row 541 of our fake data, and the log fold change is -2.25 > mean(mat[541,6:10])-mean(mat[541,1:5]) [1] -2.253898 Et voila! Same exact log fold change. Also note two things - if you are using RMA, and IMO you should be, then the data in your ExpressionSet will be log base 2. Additionally, log(A/B) == log(A) - log(B). Best, Jim > So can I take a lfc, A, M, exprs(), et cetera to get the values that the log fold change is directly calculated from? > > Sorry if this question has been asked, I have no idea how to describe my problem succinctly. > > Cheers! > Sam McInturf > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor