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How to get expression set from GSE?

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?

I tried:

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
affymetrix gse geo r
• 4,377 views • link
written by lotus28 lotus28

However, with another dataset getting exp-set is as simple as

setwd("C:\Users\user\Desktop")

source("http://www.bioconductor.org/biocLite.R")
biocLite('affy')
library(affy)

affydata <- ReadAffy(filenames='GSM910633_Human_intestinal_microbiota_1.CEL')
probes <- featureNames(affydata)
eset <- exprs(rma(affydata))
• 0 views • link
written by lotus28 lotus28

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