[BioC] Alternative to combineAffybatch

Nicolas Servant nicolas.servant at gmail.com
Mon Mar 25 15:42:41 CET 2013

Dear all,

I would like to run an old R script (R2.5) to combine some recent
HGU133A and A2 arrays.
When I try to read these new arrays with read.affybatch on R2.5 it crashes

> sapply(list.celfiles("NEW_DATA/", full.names=TRUE), read.affybatch)	
Is NEW_DATA//BC13_ARN0186_s1h1_U133A2.CEL really a CEL file? tried
reading as text, gzipped text, binary and gzipped binary.

The same command works well on R2.15 ! However, my next step is to
combine U133A and A2 arrays using

>res<-combineAffyBatch(list(pool1,pool2),c("hgu133aprobe","hgu133a2probe"), newcdf="comb")

And I just saw that the combineAffyBatch function is no more supported.
So does anyone has any idea :
1/ to fix the issu I have when I tried to read my CEL file under R2.5
2/ to give me an alternative to the combineAffyBatch function

Thank you

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