Hi BioC User, I am working for the first time on agilent CGH arrays (singel- channel). I would like to use the limma package for that> This is my script: >library(limma) >targets <- readTargets("targets.txt") >x <- read.maimages(targets, path="rawData/", source="agilent",green.only=TRUE, names = targets$condition) >RG <- read.maimages(targets, path="rawData/", columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "gProcessedSignal", Rb = "gIsPosAndSignif"), annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName"), names = targets$condition) I tried both examples as I've found an explanation mentioning both of them ( here<http: matticklab.com="" index.php?title="Single_channel_analysis_of_" agilent_microarray_data_with_limma="">). My problem is that the results differs slightly from one another: > RG An object of class "RGList" $G controll 5_4_chr5 5_3_chr5 5_4_cp 5_3_growth 5_3_cp 5_3_growth [1,] 363.0 374.0 1647 678.0 498.5 505.0 642 [2,] 34.0 24.0 27 34.5 31.0 34.0 31 [3,] 29.5 23.0 23 30.0 26.0 26.5 30 [4,] 31.0 23.0 28 28.0 27.0 31.0 29 [5,] 31.0 25.5 28 27.0 32.0 29.0 31 45209 more rows ... > x An object of class "EListRaw" $E controll 5_4_chr5 5_3_chr5 5_4_cp 5_3_growth 5_3_cp 5_3_growth [1,] 361.30160 364.68250 1667.98200 683.31250 506.46670 502.66670 649.01610 [2,] 34.84483 25.94737 29.00000 35.54839 32.28571 33.16949 30.70492 [3,] 31.23438 25.46032 23.61905 31.90164 27.84127 28.95161 30.82540 [4,] 31.65000 24.31818 27.72414 31.83607 28.85484 31.39683 30.25000 [5,] 32.06349 25.93548 28.98413 28.25000 31.44615 28.04615 30.78462 45209 more rows ... Even though the differences are very small, I would still like to understand them. If I understood the manual correctly, limma takes by default the median column for both fore- and background. The background values are similar (x$Eb and RG$Eb). What columns does limma uses for the analysis? I would appreciate the help thanks Assa > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.10.3 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tools_2.14.1 [[alternative HTML version deleted]]