[BioC] chickencdf in qcEnv

[Lina Hultin-Rosenberg]

Hi!

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
project/Data/QC/AP009_chicken_qc_report.pdf")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
........................done.
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