[BioC] simpleaffy 2.14.02, setQCEnvironment

[Crispin Miller]

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
>>
 
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