
Hi Dear BioC
I have question about design matrix considering the batch effect using limma.  The experiment design is a factorial design.
 Experiment (Affy chip)
        Array     Strain  Treatment  Replicate  Batch
        1        A        No         1          1
        2        A        No         2          1
        3        A        No         3          1
        4        A        Yes        1          1
        5        A        Yes        2          1
        6        A        Yes        3          1
        7        B        No         1          2
        8        B        No         2          2
        9        B        No         3          2
        10       B        Yes        1          2
        11       B        Yes        2          2
        12       B        Yes        3          2
 Here we want to konw which genes respond differently in treated vs. untreated, and we also want to find out the interaction.   However, the cluster analysis showed that there is a clear batch effect.  So I designed the following design matrix to remove the
batch effect:
design
             A_unTrt  A_Trt    B_unTrt  B_Trt    Batch
        1    1        0        0        0        0
        2    1        0        0        0        0
        3    1        0        0        0        0
        4    0        1        0        0        0
        5    0        1        0        0        0
        6    0        1        0        0        0
        7    0        0        1        0        1
        8    0        0        1        0        1
        9    0        0        1        0        1
        10   0        0        0        1        1
        11   0        0        0        1        1
        12   0        0        0        1        1
 
contrast <- makeContrasts(
       TrtvsUntrt=(A_Trt+B_trt)-(A_unTrt+B_unTrt),
       interaction=(A_Trt-A_unTrt)-(B_Trt-B_unTrt),
       levels=design)
However, when I tried to fit the data and the following happes
 fit <- lmFit(myData, design)
Coefficients not estimable: Batch 
I am using limma version 2.10.5 and R version 2.5.1
 
Any suggestions?
 
Many thanks,
 
Jason
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