Summing up prob level

Question

[zizigolu]

Hi

I have normalized a microarray data and matched the prob identifiers to gene symbol but now for some genes I have several probes. For example for gene A I have several matched probes. So I have repetition for gene A. How I can take mean over the expression of repeated genes please and having an unique value?

This is my expression matrix

> head(array[,1:10,1:5])
               GSM482796 GSM482797 GSM482798 GSM482799
1         OR2T6    0.0171   -0.1100   -0.0394   -0.0141
2          EBF1    0.1890    0.0222    0.0832    0.0459
3 DKFZp686D0972    1.9400    0.2530    0.3770    0.8310
4        ATP8B4   -0.1490    0.0690   -0.0637   -0.0527
5      NOTCH2NL    0.1540   -0.3880    0.2160   -0.0812
6        SPIRE1    0.2920    0.1690    0.5500    0.1430

Answer 1

[zizigolu]

> limma::avereps(array,ID=rownames(array))

[Kevin Blighe]

That is correct.

[zizigolu]

@Kevin you thought me limma::avereps function in my previous query if not I was wandering in google without getting the answer

Thank you

[Kevin Blighe]

No problem