#Extract probe ids, entrez symbols, and entrez ids Ls('package:hugene10sttranscriptcluster.db') #Annotations at the transcript-cluster level (more gene-centric view) Ls('package:hugene10stprobeset.db') #Annotations at the exon probeset level #To see all available mappings for this platform #Map probe sets to gene symbols or other annotations #Get the important stuff out of the data - the expression estimates for each array #perform RMA normalization (I would normally use GCRMA but it did not work with this chip) Raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname='hugene10stv1') #From bioconductor Setwd('/Users/ogriffit/Dropbox/BioStars/GSE27447/data') Sapply(paste('data', cels, sep='/'), gunzip)

Setwd('/Users/ogriffit/Dropbox/BioStars/GSE27447')Ĭels = list.files('data/', pattern = 'CEL') #Download the CEL file package for this dataset (by GSE - Geo series id) Setwd('/Users/ogriffit/Dropbox/BioStars') # install additional bioconductor libraries, if not already installedīiocLite('hugene10sttranscriptcluster.db') #install the core bioconductor packages, if not already installed It assumes you have latest version of R installed and will have to change some working directories. This is how I would process that particular dataset in R/Bioconductor.

Reading cdf files r