Entering edit mode
8.0 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
However, with another dataset getting exp-set is as simple as
setwd("C:\Users\user\Desktop")