I have been trying to read cel files from NCBI website and have been having problems. I was able to read the cel files using getGEO() using R version 2.14.0 but the problem is i need the matchprobe library which only works under R version 2.11. So i switched to R version 2.11 but I just keep getting the following error using the getGEO() : Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between assayData and featureData. So instead i tried using the Readaffy() from the affy() library but i got the following error: cannot allocate vector of size 470.1. I tried increasing the memory using the memory.size() but it doesn't work. I have alot of space on the directory. If i use the rma, it will get the expressions and perform rma and i don't want that. Any help or any ideas to get one of them working? -- output of sessionInfo(): R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.26.1 GEOquery_2.13.7 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 preprocessCore_1.10.0 RCurl_1.4-2 [4] tools_2.11.1 XML_3.2-0 -- Sent via the guest posting facility at bioconductor.org.

Hi Salwa, On 2/6/2012 2:01 PM, Salwa [guest] wrote: > I have been trying to read cel files from NCBI website and have been having problems. I was able to read the cel files using getGEO() using R version 2.14.0 but the problem is i need the matchprobe library which only works under R version 2.11. So i switched to R version 2.11 but I just keep getting the following error using the getGEO() : Error in validObject(.Object) : > invalid class "ExpressionSet" object: featureNames differ between assayData and featureData. So instead i tried using the Readaffy() from the affy() library but i got the following error: cannot allocate vector of size 470.1. I tried increasing the memory using the memory.size() but it doesn't work. I have alot of space on the directory. If i use the rma, it will get the expressions and perform rma and i don't want that. > > > Any help or any ideas to get one of them working? I doubt you need the matchprobes package. What exactly are you trying to do? Best, Jim > > -- output of sessionInfo(): > > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.26.1 GEOquery_2.13.7 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 preprocessCore_1.10.0 RCurl_1.4-2 > [4] tools_2.11.1 XML_3.2-0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues