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 Norbyv?gen 18 752 36 Uppsala Phone: +46-18-4716444 Email: lina.hultin.rosenberg at ebc.uu.se