[BioC] affyPLM and exon array question

[Allen Day]

Thanks Ben, this is very helpful.  I'll try excluding the background
probesets to see if that speeds things up.  I'll post my findings
here.

-Allen


On 5/1/07, Ben Bolstad <bmb at bmbolstad.com> wrote:
> The slowdown you are observing is due to just a few probesets on the
> array. These probesets contain many 1000's of probes. In the current
> implementation when you use the command that you specified (fitting the
> default model) fitPLM uses a procedure optimized for probesets with
> relatively few probes across many arrays and so is pretty quick most of
> the time (my experience is that is is not completely unacceptable even
> up to about 1000 probes across a large number of arrays, at least on my
> machine).
>
> eg both of the following contain same number of datapoints
>
> Case I: 11 probes and 1000 arrays
> Case II: 1000 probes and 11 probes
>
> but case I will be a lot quicker than case II in the current
> implementation.
>
> Demonstration code
>
> > library(affyPLM)
>
> ### note to any developers out there, the following is UNSUPPORTED
> ### and subject to change. DO NOT USE.
> > rlm.default.rma.model <- function(y,PsiCode=0,PsiK=1.345){
> +   .Call("R_rlm_rma_default_model",y,PsiCode,PsiK,PACKAGE="affyPLM")
> + }
>
> #Case I
> > y <- matrix(rnorm(11*1000),11,1000)
> > system.time(test <- rlm.default.rma.model(y))
> [1] 0.735 0.032 0.788 0.000 0.000
>
> #Case II
> > y <- matrix(rnorm(11*1000),1000,11)
> > system.time(test <- rlm.default.rma.model(y))
> [1] 19.776  0.508 21.730  0.000  0.000
>
> As for workarounds, I am pretty sure that these extremely large
> probesets are control probesets of some kind that could be safely
> ignored and it is possible to pass a vector of probeset names specifying
> a subset to use for fitPLM.
>
> Best,
>
> Ben
>
> On Tue, 2007-05-01 at 12:36 -0700, Allen Day wrote:
> > 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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