I have a microarray gene expression matrix like this by weird gene IDs in rows.
> head(mat[1:10,1:5])
> dim(mat)
[1] 39302 76
>
There is matched gene symbol for each of these identifiers in another matrix
>
> dim(matched)
[1] 23107 1
>
How I can have matched gene symbol with probe identifiers in the row names of my expression matrix please? The problem is, for one gene symbol we may I tried
> merged <- merge(mat, matched)
Error: cannot allocate vector of size 6.8 Gb
EDITED
tmp = paste(matched[rownames(mat)],rownames(mat),sep="_")
> rownames(mat) = tmp
EDITED
This is my matrix after matching prob identifiers to gene symbol
> 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
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?
dput(head(matched))
? $\endgroup$