[BioC] affyPLM and exon array question

[Allen Day]

Hi,

I've been trying to get NUSE, RLE, and RMA values for HuEx-1_0-st-v2
(Human "all exon") Affymetrix arrays.

So far I have successfully read the arrays into an affybatch object.
This required creating the CDF environment, which I have already done
with makecdfenv.  I'll be submitting that for inclusion shortly, but
that's another topic.

After creating the AffyBatch, I try to use affyPLM to do an RMA model
fit.  R = 2.4.1, affyPLM = 1.12.0, affy = 1.12.2.  That's where
there's trouble, and it appears to be caused by the lack of mismatch
probes on the array.  Here's code illustrating the problem:

> library( 'affy' );
> library( 'affyPLM' );
> ab = read.affybatch( filenames='/home/allenday/cel/0001.CEL' );
> ab; # works, output omitted
> pm( ab ); # works, output omitted
> mm( ab ); # fails!
Error in FUN(X[[1411190]], ...) : subscript out of bounds
> plm = fitPLM( ab ); #same failure in fitPLM, caused by a call to mm() on variable ab;
Error in FUN(X[[1411190]], ...) : subscript out of bounds

I'm only proficient enough in R and C to track this down -- I'm don't
know R or Bioconductor well enough to know how to fix it.  If I can
get this going I will submit a new package that provides just.nuse()
and just.rle() functions.  Can someone give me a pointer for how to
make this work?

Thanks.

-Allen