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)
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