Hi,

I am attempting to process a few Agilent 4x44 based arrays using limma. When I try to estimate expression levels with lmFit in limma, I get the following message:

Warning message:
In lmFit(MA, method = "robust") :
Some coefficients not estimable: coefficient interpretation may vary.

And all the coeff's are NA. I am not at all sure what the problem is? Can someone give me an idea?

Code snipet:

#Normalize data with background subtraction
        MA<-normalizeWithinArrays(RG.Nctr , method="loess", bc.method="rma" )
        MA<-normalizeBetweenArrays(MA , method="quantile")

        #get exp values
        fit <- lmFit(MA)

Thanks,
Aaron


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