Thanks a lot Jim for your quick response! James W. MacDonald wrote: > Hi Xingmei, > > Xingmei Wang wrote: >> My code is as following: >>> setwd("G:/XWang/microarray_phototherapy/CEL file") >>> library(affyQCReport) >> Loading required package: Biobase >> Loading required package: tools >> Welcome to Bioconductor >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> Loading required package: affy >> Loading required package: simpleaffy >> Loading required package: genefilter >> Loading required package: survival >> Loading required package: splines >> Loading required package: gcrma >> Loading required package: matchprobes >> Loading required package: xtable >> Loading required package: affyPLM >> Loading required package: preprocessCore >> Loading required package: RColorBrewer >> Loading required package: geneplotter >> Loading required package: lattice >> Loading required package: annotate >> Loading required package: AnnotationDbi >> KernSmooth 2.22 installed >> Copyright M. P. Wand 1997 >>> mydata<-ReadAffy() >>> QCReport(mydata, file="GelfandQC.pdf") >> Error in getCdfInfo(object) : Could not obtain CDF environment, >> problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> Any suggestion would be highly appreciated! > > The affyQCReport uses the affy package for doing the analysis. > Unfortunately, the affy package doesn't support the HuGene chips. To > analyze these chips you need to use either oligo or xps. I'm still new in this field, so will need to do some reading on what you suggested. Thanks again! > > Best, > > Jim > > >> Xingmei >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Xingmei wang , MS Biostatistician Biostatistics Analysis Center (BAC) University of Pennsylvania School of Medicine Center for Clinical Epidemiology and Biostatistics 519 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104 Phone: 215-898-1560 Fax: 215-573-1203 Email: xwang5 at mail.med.upenn.edu Website: http://www.cceb.med.upenn.edu/services/bac/