[BioC] gcrma

[Chris Paulse]

I get similar results:

>rawData <- ReadAffy()
>eset <- gcrma(rawData)
Loading required package: rgu34aprobe
background correction: gcrma
normalization: quantiles
PM/MM correction : pmonly
expression values: medianpolish
background correcting...Error in tmp[1, ] : incorrect number of dimensions
In addition: Warning messages:
1: NaNs produced in: log(x)
2: NaNs produced in: log(x)
3: NaNs produced in: log(x)
4: NaNs produced in: log(x)

Chris


>From: "Rafael A. Irizarry" <ririzarr at jhsph.edu>
>Reply-To: rafa at jhu.edu
>To: Crispin Miller <CMiller at picr.man.ac.uk>
>CC: "Bioconductor \(E-mail\)" <bioconductor at stat.math.ethz.ch>
>Subject: Re: [BioC] gcrma
>Date: Sun, 03 Aug 2003 19:50:45 -0400 (EDT)
>
>what is the class of eset? gcrma operates on instances of class AffyBatch.
>
>On Fri, 1 Aug 2003, Crispin Miller wrote:
>
> > Hi,
> > I've been trying to play with gcrma...
> > When I chuck an affyBatch object, eset,  at it (containing 25 U133A 
>arrays) as follows:
> >
> > > normalised <- gcrma(eset)
> > It gets as far as background correcting and then dies with:
> >
> > Error in tmp[1, ] : incorrect number of dimensions
> > and then a few warning messages:
> >
> > NaNs produced in log(x)
> >
> > I get the same if I try different normalisation techniques or mle 
>instead of eb...
> >
> >  I have installled both the hgu133aprobe and the matchprobes 
>libraries...
> >
> > I was wondering if anyone can help?
> >
> > Cheers,
> > Crispin
> >
> > --------------------------------------------------------
> >
> >
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>o...{{dropped}}
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