problem in ReadAffy function (affy and affyio libraries)
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@groot-philip-de-1307
Last seen 8.4 years ago
Hello all, I am working with the Affymetrix GeneTitan Gene ST plates ("mogene11stv1" arrays). Information on these arrays via the Affymetrix website: http://www.affymetrix.com/support/technical/byproduct.affx?product =MoGene-1_1-st-v1 When using the "affy" library to load the .CEL-files, I obtain the following AffyBatch object: > x <- ReadAffy() > x AffyBatch object size of arrays=990x1190 features (20 kb) cdf=MoGene-1_1-st-v1 (35556 affyids) number of samples=9 number of genes=35556 annotation=mogene11stv1 notes= Please notice that the "size of arrays" is wrong: x and y have been switched. When I use the "affxparser" library to obtain the "size of arrays" things work out fine: > library(affxparser) > celHead <- readCelHeader(list.celfiles()[1]) > c(celHead$rows, celHead$cols) [1] 1190 990 Now the "size of arrays" is correct. I located the problem in the ReadAffy() function in the following line: function: read.celfile.header (called from within the ReadAffy function) headdetails <- .Call("ReadHeader", filename, PACKAGE = "affyio") As you can see, the actual problem is in the affyio library, where the .Call() command returns an inappropriate "headdetails" object. Consequently, the dimensions of "exprs(AffyBatch)", after loading the .CEL-files, is also wrong. Note that for the Gene ST version 1.0 arrays the above is not a problem because the arrays are square. The Gene ST arrays version 1.1 are rectangularly defined. The problem is also present in R-2.10.1. Can this problem be fixed please? > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affxparser_1.20.0 mogene11stv1cdf_2.1.0 affy_1.26.0 [4] Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.0 Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot at wur.nl<mailto:philip.degroot at="" wur.nl=""> Internet: http://www.nutrigenomicsconsortium.nl<http: www.nutrigenomi="" csconsortium.nl=""/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/
affyio affyio • 983 views
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