How to get expression set from GSE?
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Entering edit mode
6.0 years ago
lotus28 ▴ 70

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 • 3.3k views
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Entering edit mode

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))
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