[BioC] combined Affybatch and mas5

Lewin Eisele lewin.eisele at uni-essen.de
Sun Jun 18 08:33:39 CEST 2006

Dear list,

I have combined two AffyBatches with the function combineAffyBatch
of the matchprobes package. 10 samples were hybridized to hgu133plus2
chips and 15 to hgu133a chips. Now I would like to compute MAS5
expression values for the combined AffyBatch. However, a call to the
function mas5 of the affy package produces an error:

 > ab.comb
AffyBatch object
size of arrays=0x0 features (94474 kb)
cdf=combcdf (22280 affyids)
number of samples=25
number of genes=22280

 > mas5(ab.comb)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...Error in as.vector(data) : NAs in foreign 
function call (arg 2)
In addition: Warning message:
NAs introduced by coercion

The problem seems to be that the combined AffyBatch has no
dimensions and therefore the lines

     allx <- c(pm.index, mm.index)%%nrow(object)
     allx[allx == 0] <- rows
     ally <- c(pm.index, mm.index)%/%nrow(object) + 1

in the function bg.correct.mas of affy produce NaN for allx.
Is there a way to circumvent this, e.g. give (virtual) dimensions
to the combined AffyBatch?

I'm aware that the how-can-I-get-MAS5-expression-values-with-combined-
AffyBatches question has already been asked, however I couldn't
find a solution in the mailing list archive. Is there one?


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