[BioC] chickencdf in qcEnv

Lina Hultin-Rosenberg Lina.Hultin.Rosenberg at ebc.uu.se
Thu Jul 20 11:49:23 CEST 2006


I am working on some chicken affymetrix data and would like to generate a QC
report for the chips. When using the QCReport function I get an error
message (see below) and when looking at qcEnv it seems as if the chickencdf
is not included (see below).

> QCReport(affydata,file="/home/lina/Microarray
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
scaling to a TGT of 100 ...
Scale factor for: PA009_kyckling_16H_060630.CEL 1.25136165168290

 for the rest of the chips
Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip
type: chickencdf
Error in plot(qc(object)) : unable to find the argument 'x' in selecting a
method for function 'plot'
> rownames(get("alpha",envir=.qcEnv))
 [1] "atgenomecdf"    "ath1121501cdf"  "drosgenome1cdf" "hcg110cdf"
 [5] "hgfocuscdf"     "hgu133acdf"     "hgu133a2cdf"    "hgu133atagcdf"
 [9] "hgu133bcdf"     "hgu133plus2cdf" "hgu95acdf"      "hgu95av2cdf"
[13] "hgu95bcdf"      "hgu95ccdf"      "hgu95dcdf"      "hgu95ecdf"
[17] "mgu74acdf"      "mgu74av2cdf"    "mgu74bcdf"      "mgu74bv2cdf"
[21] "mgu74ccdf"      "mgu74cv2cdf"    "mouse4302cdf"   "moe430acdf"
[25] "mouse430a2cdf"  "mouse430b2cdf"  "mu11ksubacdf"   "mu11ksubbcdf"
[29] "porcinecdf"     "rae230acdf"     "rae230bcdf"     "rgu34acdf"
[33] "rgu34bcdf"      "rgu34ccdf"      "ygs98cdf"       "zebrafishcdf"
[37] "rat2302cdf"

The chickencdf package is available at bioconductor and installed at my
computer, I also loaded the library before running the qc analysis.

Can I add the chickencdf to cqEnv in some way?

Thank you!

Best regards,
Lina Hultin Rosenberg
Lina Hultin Rosenberg
Msc Molecular Biotechnology
Evolutionary Biology Department
Uppsala University
Norbyvägen 18
752 36 Uppsala
Phone: +46-18-4716444
Email: lina.hultin.rosenberg at ebc.uu.se

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