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Question: Getgeo Error
0
gravatar for nazaninhoseinkhan
7.1 years ago by
nazaninhoseinkhan • 410
Iran, Islamic Republic Of
nazaninhoseinkhan • 410 wrote:

Hi all, I've just started to import gene expression data sets in R. When I try to import data using this command:

gds<-getGEO(filename=system.file("extdata/GDS2478.soft.gz",package="GEOquery"))

I get this error:

Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument
In addition: Warning messages:
1: In file(fname, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
2: In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
3: In file(fname, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former

I've searched internet for a useful guide, but unfortunately I have not been successful so far. I will appreciate any help. Nazanin
geo bioconductor • 3.0k views
ADD COMMENT • link •
modified 7.1 years ago by Sean Davis ♦ 26k • written 7.1 years ago by nazaninhoseinkhan • 410

Edited tags for you. Trust me, "question" is not a useful tag :)

ADD REPLY • link written 7.1 years ago by Neilfws ♦ 49k
1
gravatar for Neilfws
7.1 years ago by
Neilfws ♦ 49k
Sydney, Australia
Neilfws ♦ 49k wrote:

I suspect that you are copy-pasting from an old version of the GEOquery tutorial and the file GDS2478.soft.gz does not exist on your system.

Some suggestions:

  • the example GDS in the latest version of GEOquery is GDS507.soft.gz - try that instead
  • find the directory GEOquery/extdata on your system and see what example data files it contains
  • get the data direct from GEO using getGEO("GDS2478") (or another GEO identifier)
ADD COMMENT • link modified 7.1 years ago • written 7.1 years ago by Neilfws ♦ 49k
1
gravatar for Sean Davis
7.1 years ago by
Sean Davis ♦ 26k
National Institutes of Health, Bethesda, MD
Sean Davis ♦ 26k wrote:

I admit, the error is not very clear--I'll have to fix that. You are telling GEOquery to get a file from your disk that does not exist. To do what you want to do, try this:

gds = getGEO('GDS2478')
ADD COMMENT • link written 7.1 years ago by Sean Davis ♦ 26k
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