Question: Getgeo Error
gravatar for nazaninhoseinkhan
7.1 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan410 wrote:


I turned off the firewall. This time the command gds = getGEO('GDS2478') resulted in the following error:

Using locally cached version of GDS2478 found here:

Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument


bioconductor • 3.9k views
ADD COMMENTlink modified 4.5 years ago by Satyajeet Khare1.6k • written 7.1 years ago by nazaninhoseinkhan410

This works fine on my system. What's the output of sessionInfo()? Presumably you need to update something.

ADD REPLYlink written 7.1 years ago by Devon Ryan98k
gravatar for Neilfws
7.1 years ago by
Sydney, Australia
Neilfws49k wrote:

The message "Using locally cached version..." means that getGEO() is not fetching the file from GEO, but trying to use a local file on your machine.

Presumably, something is wrong with that file (e.g. it is incomplete). Delete it and try again.

ADD COMMENTlink written 7.1 years ago by Neilfws49k
gravatar for Satyajeet Khare
4.5 years ago by
Satyajeet Khare1.6k
Pune, India
Satyajeet Khare1.6k wrote:

We replaced

gset <- getGEO("GSE####", GSEMatrix =TRUE, AnnotGPL=FALSE)


gset <- getGEO("GSE####", GSEMatrix =TRUE, destdir= "/myDirectory/", AnnotGPL=FALSE)

And its working!

ADD COMMENTlink written 4.5 years ago by Satyajeet Khare1.6k
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