Question: Error in R for microarray data analysis in GEOquery
0
gravatar for ali.kian.saei
5 months ago by
ali.kian.saei10 wrote:

I want download data from GEO with GEOquery in R but I can not.

the error is

Error in file.exists(destfile) : object 'destfile' not found

my code is:

gset <- getGEO("GSE9476", GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "data/"

how can I solve error?

microarray geoquery • 217 views
ADD COMMENTlink modified 5 months ago by Kevin Blighe70k • written 5 months ago by ali.kian.saei10
0
gravatar for Kevin Blighe
5 months ago by
Kevin Blighe70k
Republic of Ireland
Kevin Blighe70k wrote:

Dear ali.kian.saei,

The problem is that there is no directory called 'data' under your current working directory. You can determine what is your current working directory by typing:

getwd()

If you want to download the series matrix file to a directory called 'data', then you need to do:

dir.create('data')
gset <- getGEO("GSE9476", GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "data/")

Or, you can also download the series matrix to a temporary location managed by your operating system via:

library(Biobase)
library(GEOquery)
gset <- getGEO("GSE9476", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL96", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

gset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 64 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM239170 GSM239323 ... GSM240509 (64 total)
  varLabels: title geo_accession ... Source:ch1 (51 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 17910043 
Annotation: GPL96

Kevin

ADD COMMENTlink modified 5 months ago • written 5 months ago by Kevin Blighe70k

hi Kevin i do what you say but i see this error

dir.create('data')

gset <- getGEO("GSE9476", GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "data/")

Error in getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, : unused argument (parseCharacteristics = parseCharacteristics)

best

ADD REPLYlink written 5 months ago by ali.kian.saei10

Please restart your computer, re-install GEOquery, and then try again.

ADD REPLYlink written 5 months ago by Kevin Blighe70k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1017 users visited in the last hour
_