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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