I'm trying to use the U133A spike-in data set (Latin square data) to do some analyses. However, I can not load the cel files into R. I installed HG-U133A_tag_CDF.zip in R using "install package from local zip file" option, but still got the following error message. Does anyone know what's wrong? > install.packages("E:/data/Liu/microarray/U133/HG-U133A_tag_CDF.zip", .libPaths()[1], CRAN = NULL) updating HTML package descriptions > testData<-ReadAffy(widget=TRUE) Loading required package: tkWidgets Loading required package: tcltk Warning messages: 1: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) 2: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) 3: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) > Your comments will be highly appreciated. Wenlei

Wenlei Liu wrote: >I'm trying to use the U133A spike-in data set (Latin square data) to do some analyses. However, I can not load the cel files into R. I installed HG-U133A_tag_CDF.zip in R using "install package from local zip file" option, but still got the following error message. Does anyone know what's wrong? > > > >>install.packages("E:/data/Liu/microarray/U133/HG-U133A_tag_CDF.zip", .libPaths()[1], CRAN = NULL) >> >> This looks like you are trying to install the cdf file you got from Affymetrix (which is incorrect). You need to do this: library(reposTools) install.packages2("hgu133atagcdf") HTH, Jim >updating HTML package descriptions > > >>testData<-ReadAffy(widget=TRUE) >> >> >Loading required package: tkWidgets >Loading required package: tcltk >Warning messages: >1: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) >2: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) >3: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) > > > >Your comments will be highly appreciated. > >Wenlei > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- James W. MacDonald Affymetrix and cDNA Microarray Facility University of Michigan Comprehensive Cancer Center 1500 E. Medical Center Drive Ann Arbor MI 48109