drosophila2cdf in simpleaffy / affyQCReport
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Assa Yeroslaviz ★ 1.5k
Last seen 21 days ago
Munich, Germany
Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_5_at ratio actin3/actinM AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_M_f_at ratio gapdh3/gapdh5 AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_5_at ratio gapdh3/gapdhM AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_M_at this I copied as drosophila2cdf.qcdef to the cirectory: ../R/x86_64-pc-linux-gnu- library/2.12/simpleaffy/extdata/drosgenome2cdf.qcdef I than try to run the analysis again: > data <- ReadAffy() > data AffyBatch (storageMode: lockedEnvironment) assayData: NA features, NA samples element names: exprs protocolData sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL (12 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL (12 total) varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: drosophila2 when I start the analysis I get the following error message: > QCReport(data) Error in setQCEnvironment(cdfn) : Could not find array definition file ' drosophila2cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. So I try to set the QCEnvironment but somehow I always get an error message: > setQCEnvironment("drosophila2cdf", "../R/x86_64-pc-linux-gnu-library/2.12/simpleaffy/extdata")Error in file(fn, "r") : cannot open the connection In addition: Warning message: In file(fn, "r") : cannot open file '../R/x86_64-pc-linux-gnu- library/2.12/simpleaffy/extdata/drosophila2cdf.qcdef': No such file or directory > Is there anything I am missing? I would appriciate any help I can get as to resolve the problem. I read in an earlier posting to the mailing list the same problem, which was supposed to be fixed with version 2.14 of simpleaffy. I am using version 2.26.0 of simpleaffy and 1.28.0 of affyQCReport. thanks in advance, Assa -- > R.version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 12.0 year 2010 month 10 day 15 svn rev 53317 language R version.string R version 2.12.0 (2010-10-15) [[alternative HTML version deleted]]
cdf simpleaffy affyQCReport cdf simpleaffy affyQCReport • 760 views

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