Getgeo Error

Question

[nazaninhoseinkhan]

Hi

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:

C:\Users\Asus\AppData\Local\Temp\Rtmpw96aum/GDS2478.soft.gz 
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument

Nazanin

[Devon Ryan]

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

Answer 1

[Neilfws]

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.

Answer 2

[Satyajeet Khare]

We replaced

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

with

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

And its working!