1) read an affybatch 2) want to show an affybatch
affybatch <-
ReadAffy(filenames=dir('../Results',pattern='.CEL'),celfile.path='../Results')
affybatch
Warning: unable to access index for repository http://bioconductor.org/packages/1.9/bioc/bin/macosx/powerpc/contrib/2.4 Warning: unable to access index for repository http://bioconductor.org/packages/1.9/data/annotation/bin/macosx/powerpc/cont rib/2.4 Warning: unable to access index for repository http://bioconductor.org/packages/1.9/data/experiment/bin/macosx/powerpc/cont rib/2.4 Warning: unable to access index for repository http://bioconductor.org/packages/1.9/omegahat/bin/macosx/powerpc/contrib/2.4 Warning: unable to access index for repository http://bioconductor.org/packages/1.9/monograph/bin/macosx/powerpc/contrib/2. 4 Warning: unable to access index for repository http://cran.fhcrc.org/bin/macosx/powerpc/contrib/2.4 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Rat230_2 Library - package rat2302cdf not installed Data for package affy did not contain rat2302cdf Bioconductor - rat2302cdf not available AffyBatch object size of arrays=834x834 features (130426 kb) cdf=Rat230_2 (??? affyids) number of samples=24 ..... I needed to install the rat cdf package by hand first. I think this is a typical problem with macos, but just wanted to make sure that I had passed it on in case someone didn't expect this to happen. Sean
sessionInfo()
R version 2.4.0 Under development (unstable) (2006-08-16 r38905) powerpc-apple-darwin8.7.0 locale: C attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: rat2302cdf affy affyio Biobase "1.12.0" "1.11.6" "1.1.3" "1.11.26"