Hi all, I've encountered trouble when using mas5calls on CEL files from YG_S98 chips: data <- ReadAffy(filenames = cel.file.name) PACalls <- mas5calls(data) Getting probe level data... Computing p-values Making P/M/A Calls Error in if (y < alpha1) { : missing value where TRUE/FALSE needed Both the release and developmental version of the 'affy' package produce this same error, but only with YG_S98 chips (same code works fine on HG-U133_Plus_2 or Mouse430_2 chips). Has anyone encountered this before? Thanks! Bruz

Upon further investigation, it appears that failure of mas5calls to work with YG_S98 chips is due to these yeast chips containing probe sets which only have 1 probe pair each. Curious about how GCOS handles these probe sets, I checked and it appears that probe sets with 1 probe pair always receive a p-value of either 0.25 or 0.75. Could a solution/work-around for this problem be implemented? I'm guessing that the person who originally wrote the code will have the best idea of how this 1 probe pair scenario ought to be dealt with. Best wishes, Bruz > Date: Mon, 20 Sep 2004 14:34:38 -0700 > From: "Bruz Marzolf" <bmarzolf@systemsbiology.org> > Subject: [BioC] mas5calls error with YG_S98 CEL files > To: <bioconductor@stat.math.ethz.ch> > Message-ID: > > <bfba7186c5b3cb4c8ea0b509fa9090b304eb01@exchange.systemsbiology.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I've encountered trouble when using mas5calls on CEL files > from YG_S98 chips: > > data <- ReadAffy(filenames = cel.file.name) > PACalls <- mas5calls(data) > > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where > TRUE/FALSE needed > > Both the release and developmental version of the 'affy' > package produce this same error, but only with YG_S98 chips > (same code works fine on HG-U133_Plus_2 or Mouse430_2 chips). > Has anyone encountered this before? > > Thanks! > Bruz

Hi, This bug is, indeed, as you say, due to probes with only one probe/pair. I'll be uploading a new version of the code next week with this fixed - I'll post to the list when it's done. I'll also be putting up an updated version of simpleaffy with rat and yeast chips added to the QC metrics. Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Bruz Marzolf Sent: 22 September 2004 20:02 To: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] mas5calls error with YG_S98 CEL files Upon further investigation, it appears that failure of mas5calls to work with YG_S98 chips is due to these yeast chips containing probe sets which only have 1 probe pair each. Curious about how GCOS handles these probe sets, I checked and it appears that probe sets with 1 probe pair always receive a p-value of either 0.25 or 0.75. Could a solution/work-around for this problem be implemented? I'm guessing that the person who originally wrote the code will have the best idea of how this 1 probe pair scenario ought to be dealt with. Best wishes, Bruz > Date: Mon, 20 Sep 2004 14:34:38 -0700 > From: "Bruz Marzolf" <bmarzolf@systemsbiology.org> > Subject: [BioC] mas5calls error with YG_S98 CEL files > To: <bioconductor@stat.math.ethz.ch> > Message-ID: > > <bfba7186c5b3cb4c8ea0b509fa9090b304eb01@exchange.systemsbiology.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I've encountered trouble when using mas5calls on CEL files from YG_S98 > chips: > > data <- ReadAffy(filenames = cel.file.name) > PACalls <- mas5calls(data) > > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where TRUE/FALSE needed > > Both the release and developmental version of the 'affy' > package produce this same error, but only with YG_S98 chips (same code > works fine on HG-U133_Plus_2 or Mouse430_2 chips). > Has anyone encountered this before? > > Thanks! > Bruz _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}