Dear List, I am using limma to analyze 2-color microarray data. After reading data from gpr files, normalize with print-tip loess, then build linear model to find the differentially expressed gene list. However, before jump to any conclusions, I want to check the mode first, whether the linear model is a good fit of the real data. The common check is residual plot to valid the model assumption. However, one residuals from stats package and one residuals.MArrayLM from limma package, basically the usages are kind of similar, residuals(object,y,..). Now I would like to extract residuals from model. I searched the BioC and R archives, and also google the web, I knew how to extract residuals using lm from R, from there I knew how to work around to extract residuals from limma model. However, there must be a easy way to exract the residuals from limma linear model. Please forgive my simple question, any comments are welcome! Best wishes, Tiandao MA <- normalizeWithinArrays(RG) # correlation between duplicates design <- modelMatrix(targets,ref="REF") corfit <- duplicateCorrelation(MA,design,ndups=4) fit <- lmFit(MA,design,ndups=4,correlation=corfit$consensus,method="ls") > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: MASS statmod limma "7.2-34" "1.3.0" "2.10.5"