Hi Zuzanna -- Zuzanna wrote: > Hello, > I have a problem with read.affy.mixed function. I want to read in > together a set of CEL files from chip types Affymettrix HGU133A_2 and > HGU133_Plus_2. I have my files to be read in in one directory together > with a white space delimited file describing them (covdesc). In this > directory I give a command:
Please ask questions about Bioconductor packages on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html my guess would be that 'covdesc' is not formatted properly, and that no files are actually merged. You might try debug(read.affy.merged) read.affy.merged() and step through as described in ?browser. Martin > >> merge <- read.affy.mixed() > Error in merged[[i]] : subscript out of bounds > Error in cdfName(merged[[i]]) : > error in evaluating the argument 'object' in selecting a method for > function 'cdfName' >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133a2.db_2.3.5 hgu133plus2probe_2.5.0 > hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6 > [5] RSQLite_0.7-3 DBI_0.2-4 > hgu133a2probe_2.5.0 AnnotationDbi_1.8.1 > [9] hgu133a2cdf_2.5.0 hgu133plus2cdf_2.5.0 > simpleaffy_2.22.0 gcrma_2.18.0 > [13] genefilter_1.28.2 affy_1.24.2 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 annotate_1.24.0 Biostrings_2.14.8 > IRanges_1.4.9 > [5] preprocessCore_1.8.0 splines_2.10.0 survival_2.35-7 > tools_2.10.0 > [9] xtable_1.5-6 > > Thanks for your help! > Zuza > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
