crispin and chris, this was a bug. jean wu (the author of the package) found it and fixed it. the fix is in version 0.4.0. because hgu95a has probes with no sequence the code assumed this was true for other chips. its not! thanks for the bug report. keep em coming. -r On Sun, 3 Aug 2003, Rafael A. Irizarry wrote: > 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@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >

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@jhsph.edu> > >Reply-To: rafa@jhu.edu > >To: Crispin Miller <cmiller@picr.man.ac.uk> > >CC: "Bioconductor \(E-mail\)" <bioconductor@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@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >