[BioC] affyPLM and exon array question

[Allen Day]

I suspect so, although I haven't tried running rma() directly.
Just.rma() works fine, and fitPLM is able to RMA normalize internally.

I was able to move this a little further along by patching the mm()
function to return empty list in the case of a dimensionless pset
variable.  Apparently it is usually a two-column matrix with pm in
psets[,1] and mm in psets[,2].  Heres the patch.
http://paste.turbogears.org/paste/1253/plain

This allows me to successfully background correct and normalize with
RMA through wrapper function fitPLM from the affyPLM library.  It's
taking forever though, even running with minimal options.  Here's my
call:

fitPLM(ab, output.param=list(residuals=FALSE,weights=FALSE,resid.SE=FALSE),verbosity.level=10);

Any advice?

-Allen

On 5/1/07, Crispin Miller <CMiller at picr.man.ac.uk> wrote:
> Hi Allen,
> Does rma() work with your cdf?
>
> We've also produced one that works OK with rma() (see the 'exonmap'
> package vignette for more details, including how to get it).  Don't know
> if that helps?
>
> Crispin
>
>
>
>
> > -----Original Message-----
> > From: bioconductor-bounces at stat.math.ethz.ch
> > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Allen Day
> > Sent: 01 May 2007 01:32
> > To: bioconductor at stat.math.ethz.ch
> > Subject: [BioC] affyPLM and exon array question
> >
> > 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
> >
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