Hello, I am trying to read and work with data from an Affymetrix tiling array. (And appreciate the previous posts for working with such data)! I am using the packages "makePlatformDesign" and "oligo". I have successfully used the makePDpackage function to create the needed package (pd.at35b.mr.v04.2.tigrv5) makePDpackage("At35b_MR_v04-2 _TIGRv5.bpmap", type="tiling", manufacturer="affymetrix") However, when using oligo to read my CEL files, I run into a problem. test<-read.celfiles("T1_R1.cel") Gayla, The oligo package and read.celfiles function retrieve the package name for the data from the header in the CEL files and attaches a pd. to the front it of. Therefor when you create your package you must also name it the same thing. Here it is informing you that it is looking for the pd.at35b.mr.v04 package, simple name your package pd.at35b.mr.v04 in the extra parameter when you use makePDpackage function makePDpackage(designFile=designFile), file1=file1, file2= file2, manufacturer="affymetrix", type="tiling", genomebuild=genomebuild, extra = list("packagename"="pd.at35b.mr.v04", "cdf.path"=cde.path, "package.path"=pathtopackage, "author"="me", "maintainer"="me <me at="" wsu.edu="">", "version"="1.0.0", "unlink"=TRUE, "verbose"=TRUE)) or simply read.celfiles("T1_R1.cel",pkgname="pd.at35b.mr.v04.2.tigrv5") Matt Settles Bioinformatician Bioinformatics Core School of Molecular Biology Department of Animal Sciences Washington State University Pullman, WA >I get the following Error message: >Loading required package: pd.at35b.mr.v04 >Error: invalid version specification > >I've also tried installing the package directly >install.packages("pd.at35b.mr.v04.2.tigrv5", repos=NULL) > >And get the following errors: >Warning in install.packages("/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5", : > argument 'lib' is missing: using '/home/server/uid/R_LIBS' >ERROR: cannot install to srcdir >Warning message: >In install.packages("/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5", : >installation of package '/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5' had non-zero exit status > >One final thing I did notice is the package created by makePlatformDesign is pd.at35b.mr.v04.2.tigrv5, which is slightly different than the package it tries to load under the read.celfiles function >(pd.at35b.mr.v04). > > >Any ideas or suggestions for how I can use the package I created to read my cel files would be appreciated. My sessionInfo() is pasted below. > >Thank you, >-Gayla Olbricht