Hello, I am running R-2.5; Bioconductor 2.0 and oligo 1.0.2-3. I have created a SNPQset but am unable to get the genotypes from crlmm: > hindcrlmm = crlmm(hindDataRMA,correctionFile ="correctionHind.rda") M correction not provided. Calculating. Will take several minutes. Error: number of cluster centres must lie between 1 and nrow(x) This is a test set of 2 chips. Thanks for your help, Beth

add the gender associated to the 2 samples in the phenoData slot of hindDataRMA and this problem will be taken care of. b On Jun 5, 2007, at 6:50 PM, Beth Wilmot wrote: > Hello, > > I am running R-2.5; Bioconductor 2.0 and oligo 1.0.2-3. > > I have created a SNPQset but am unable to get the genotypes from > crlmm: > >> hindcrlmm = crlmm(hindDataRMA,correctionFile ="correctionHind.rda") > M correction not provided. Calculating. Will take several minutes. > Error: number of cluster centres must lie between 1 and nrow(x) > > This is a test set of 2 chips. > > > Thanks for your help, > Beth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

hit 'send' before adding an example, sorry. say your first sample is 'male' and the second is 'female': samples = sampleNames(hindDataRMA) df = data.frame(gender=c("male", "female"), row.names=samples) md = data.frame(labelDescription="gender of the sample", row.names="sample") phenoData(hindDataRMA) = new("AnnotatedDataFrame", data=df, varMetadata=md) best, b On Jun 5, 2007, at 6:50 PM, Beth Wilmot wrote: > Hello, > > I am running R-2.5; Bioconductor 2.0 and oligo 1.0.2-3. > > I have created a SNPQset but am unable to get the genotypes from > crlmm: > >> hindcrlmm = crlmm(hindDataRMA,correctionFile ="correctionHind.rda") > M correction not provided. Calculating. Will take several minutes. > Error: number of cluster centres must lie between 1 and nrow(x) > > This is a test set of 2 chips. > > > Thanks for your help, > Beth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor