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Question: simpleaffy 2.14.02, setQCEnvironment
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gravatar for Stefan Thomsen
11.2 years ago by
Stefan Thomsen50 wrote:
Dear all, I am trying to perform some simpleaffy analyses on Drosophila Genome 2.0 genechips. Following the instructions of the simpleaffy 2.14.02 vignette I set up the following .qcdef file: 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 I saved it as drosophila2cdf.qcdef.txt and removed the file extension .txt afterwards. When I try to run qc() on my affybatch and affybatch.mas5 (created by calling call.exprs(affybatch, "mas5") objects I get the following error message: > library(simpleaffy) Loading required package: affy Loading required package: Biobase Loading required package: tools Loading required package: affyio Loading required package: preprocessCore Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: gcrma Loading required package: matchprobes > setQCEnvironment("drosophila2cdf", "/Users/Stefan") > qc.data=qc(affybatch.raw, affybatch.mas5) 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. I confess, my programming skills are rather limited. However, I tried to look at setQCEnvironment() and its subfunction qc.read.file(). If I directly assign the .qcdef file including its path to the 'fn' argument, qc.read.file seems to be able to open, read and print the lines of my file. Thus, why do keep on running into this error? Any help on this issue would be highly appreciated. My sessionInfo is as follows: > sessionInfo() R version 2.6.0 (2007-10-03) powerpc-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] simpleaffy_2.14.02 gcrma_2.10.0 matchprobes_1.10.0 genefilter_1.16.0 survival_2.32 affy_1.16.0 [7] preprocessCore_1.0.0 affyio_1.6.0 Biobase_1.16.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.0.4 DBI_0.2-3 RSQLite_0.6-3 annotate_1.16.0 > -- Dr. Stefan Thomsen Research Associate Department of Zoology University of Cambridge Downing Street Cambridge CB2 3EJ Tel.: +44 1223 336623 Fax: +44 1223 336679 stt26 at cam.ac.uk
ADD COMMENTlink modified 11.2 years ago by Crispin Miller1.1k • written 11.2 years ago by Stefan Thomsen50
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gravatar for Crispin Miller
11.2 years ago by
Crispin Miller1.1k
Crispin Miller1.1k wrote:
Hi Stefan, I've have just fixed this - the changes will appear in version 2.14.04... Cheers, Crispin On 11/10/07 10:33, "Stefan Thomsen" <stt26 at="" cam.ac.uk=""> wrote: > Dear all, > > I am trying to perform some simpleaffy analyses on Drosophila Genome 2.0 > genechips. Following the instructions of the simpleaffy 2.14.02 vignette I > set up the following .qcdef file: > > 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 > > I saved it as drosophila2cdf.qcdef.txt and removed the file extension .txt > afterwards. > > When I try to run qc() on my affybatch and affybatch.mas5 (created by > calling call.exprs(affybatch, "mas5") objects I get the following error > message: > >> library(simpleaffy) > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > Loading required package: affyio > Loading required package: preprocessCore > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: gcrma > Loading required package: matchprobes > >> setQCEnvironment("drosophila2cdf", "/Users/Stefan") >> qc.data=qc(affybatch.raw, affybatch.mas5) > 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. > > > I confess, my programming skills are rather limited. However, I tried to > look at setQCEnvironment() and its subfunction qc.read.file(). If I > directly assign the .qcdef file including its path to the 'fn' argument, > qc.read.file seems to be able to open, read and print the lines of my file. > > Thus, why do keep on running into this error? > > Any help on this issue would be highly appreciated. > > > My sessionInfo is as follows: > >> sessionInfo() > R version 2.6.0 (2007-10-03) > powerpc-apple-darwin8.10.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: [1] simpleaffy_2.14.02 gcrma_2.10.0 > matchprobes_1.10.0 genefilter_1.16.0 survival_2.32 affy_1.16.0 [7] > preprocessCore_1.0.0 affyio_1.6.0 Biobase_1.16.0 > > loaded via a namespace (and not attached): [1] AnnotationDbi_1.0.4 > DBI_0.2-3 RSQLite_0.6-3 annotate_1.16.0 >> -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}
ADD COMMENTlink written 11.2 years ago by Crispin Miller1.1k
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