[BioC] gcrma

[Rafael A. Irizarry]

im looking into this. it probably wont get fixed till next week.


On Tue, 5 Aug 2003, Chris Paulse wrote:

> 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
> > >
> > > --------------------------------------------------------
> > >
> > >
> > > This email is confidential and intended solely for the use 
> >o...{{dropped}}
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > >
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>