Hi, I am analyzing data from a custom affy array that contains genes from several species, while the samples come from only one of the species. It seems reasonable to try the GCRMA background correction using only the features corresponding to that one species. However, the current design of the affybatches makes it impossible to subset by genes, and the bg.adjust.gcrma function does not seem to have an option to use only a subset of the genes. Any suggestions? Thank you! Omar. -- Omar De la Cruz Department of Statistics University of Chicago

> > Hi, > > I am analyzing data from a custom affy array that > contains genes from several species, while the > samples come from only one of the species. It seems > reasonable to try the GCRMA background correction > using only the features corresponding to that one > species. > > However, the current design of the affybatches > makes it impossible to subset by genes, and the > bg.adjust.gcrma function does not seem to have > an option to use only a subset of the genes. > > Any suggestions? Define your own CDF environment containing only the probes you want to be used, and associate that environment with your affybatch. However beware that with low number of genes, the estimation of parameters for gcRMA's background correction might be challenged. L. > Thank you! > > Omar. > > > -- > > Omar De la Cruz > Department of Statistics > University of Chicago > > _______________________________________________ > 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 >