I'm dealing with a dataset from GEO that is provided as a TAR archive (GSE**_RAW.tar) containing CEL files. These CEL files also include TXT files, which might contain supplementary or metadata information related to the microarray experiment.
When I try to read them on Rstudio I encounter this error:
**.CEL does not seem to have the correct dimensions.
Did someone solve this problem? Or can you suggest me a tutorial? My CEL file are from 3 platforms: Affymetrix Human X3P Array,Affymetrix Mapping 250K Nsp SNP Array and Affymetrix Mapping 250K Sty2 SNP Array.
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The affy Bioconductor package has a pretty straightforward interface for reading CEL files in and will generate an ExpressionSet as the final output.
https://www.bioconductor.org/packages/release/bioc/html/affy.html
affy.set <- ReadAffy(celfile.path = "/directory/where/files/are/saved/")
I haven't encountered those specific arrays personally so I don't know what annotation packages are available from Bioconductor for these
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I remember trying the
read.celfile()function from affyio package in R, but what worked better for me is reading the .chp file (which are the raw files from which CEL files are made IIRC) using thereadChp()function from affxparser