probe-level mean-centering of RMA normalized probes with R bioconductor

Question

I have several microarray datasets from Leukaemia and Lymphoma patients which I have normalized with rma eset <- rma (Data). I want to obtain the probe-level-mean-centring, what package can I use for that? would anyone recommend a useful and robust script to apply on my datasets? for instance:

Data <- ReadAffy (....)  #read raw CEL files
eset <- rma (Data)       #rma normalization
expr_mat <- exprs(eset)  #get expression

This will give me a table with rma normalized probes for my samples. What code can I add here to obtain log2 probe level mean centring ? Thanks!

Answer 1

NB rma data is already log2 valued. The following will mean centre by probe/row dummy data example:

> m=1:40
> dim(m)=c(10,4)
> m
      [,1] [,2] [,3] [,4]
 [1,]    1   11   21   31
 [2,]    2   12   22   32
 [3,]    3   13   23   33
 [4,]    4   14   24   34
 [5,]    5   15   25   35
 [6,]    6   16   26   36
 [7,]    7   17   27   37
 [8,]    8   18   28   38
 [9,]    9   19   29   39
[10,]   10   20   30   40

then by the magic of recycling, scale by row

> m-rowMeans(m)

      [,1] [,2] [,3] [,4]
 [1,]  -15   -5    5   15
 [2,]  -15   -5    5   15
 [3,]  -15   -5    5   15
 [4,]  -15   -5    5   15
 [5,]  -15   -5    5   15
 [6,]  -15   -5    5   15
 [7,]  -15   -5    5   15
 [8,]  -15   -5    5   15
 [9,]  -15   -5    5   15
[10,]  -15   -5    5   15