I've seen several tutorials on getting expression set from GDS. More specifically, via GEOquery. But the data I'm working with has no GDS.
How can I get the list of most highly expressed genes from a GSE-file?
setwd("C:\\Users\\user\\Desktop") source("http://www.bioconductor.org/biocLite.R") biocLite('affy') library(affy) biocLite('ecolitab520346fcdf') library(ecolitab520346fcdf) affydata <- ReadAffy(filenames='GSM2056048_stat_transcriptome.CEL') probes <- featureNames(affydata) eset <- exprs(rma(affydata))
But I get an error at
library(ecolitab520346fcdf), because there is no such package.
If I don't import anything, then I get an error at
probes <- featureNames(affydata) that goes:
Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Ecoli_TAb520346F Library - package ecolitab520346fcdf not installed Bioconductor - ecolitab520346fcdf not available