[BioC] residuals.MArrayLM

[Tiandao Li]

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"