Hello, I just noticed an odd behavior of bg.adjust.gcrma - I thought it was only supposed to change the pm values, not mm values, according to the help page: "The returned value is an 'AffyBatch' object, in which the PM probe intensities have been background adjusted. The rest is left the same as the starting 'AffyBatch' object." However, my mm values are changing (example code below) for all genes except those starting with "AFFX" on Affy's soybean chip. I also checked this behavior for some drosgenome1 chips, and there all the mm values are changing, even for "AFFX" genes. The changing mm values aren't causing me any problems, but I thought that since they weren't supposed to change I would ask about it. I came across this issue trying to figure out why my adjusted pm values change when I remove some probesets before doing bg.adjust.gcrma, but that's another posting... Thanks, Jenny > gc.abatch <- bg.adjust.gcrma(raw.data) #The first 135 genes start with "AFFX" > sum( mm( raw.data, allgenenames[1:135]) - mm(gc.abatch,allgenenames[1:135]) ==0) [1] 10680 > length( mm( raw.data, allgenenames[1:135]) - mm(gc.abatch,allgenenames[1:135])) [1] 10680 > sum( mm( raw.data, allgenenames[136:270]) - mm( gc.abatch, allgenenames[136:270]) ==0) [1] 0 > sessionInfo() Version 2.3.0 (2006-04-24) i386-pc-mingw32 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: drosgenome1cdf soybeanprobe soybeancdf made4 scatterplot3d "1.12.0" "1.12.0" "1.12.0" "1.6.0" "0.3-24" ade4 affyQCReport simpleaffy genefilter survival "1.4-1" "1.10.0" "2.6.0" "1.10.1" "2.24" reposTools affyPLM gcrma matchprobes affydata "1.10.0" "1.8.0" "2.4.1" "1.4.0" "1.8.0" affy affyio Biobase limma RWinEdt "1.10.0" "1.0.0" "1.10.0" "2.7.2" "1.7-4" > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu