getGEO error fetching data
1
0
Entering edit mode
lallo_92 • 0
@lallo_92-13983
Last seen 3.1 years ago

Hi,

 

Apologies for my ignorance as I am still an R amateur. Currently, I am trying to access a GEO dataset using the sample code that is computed via GEO2R. However, I stumble upon issues already on line 1 with the error message below:

 

gset <- getGEO("GSE13995", GSEMatrix =TRUE, AnnotGPL=FALSE)

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE13nnn/GSE13995/matrix/
Found 2 file(s)
GSE13995-GPL7752_series_matrix.txt.gz
Using locally cached version: /var/folders/58/cm6szd7s045g4z6dbtqzdyh80000gn/T//RtmpzJ4fko/GSE13995-GPL7752_series_matrix.txt.gz
Using locally cached version of GPL7752 found here:
/var/folders/58/cm6szd7s045g4z6dbtqzdyh80000gn/T//RtmpzJ4fko/GPL7752.soft 
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument

 

Some help would be greatly appreciated. Thank you in advance!

 

Ralitsa 

 

 

 

geoquery error message • 504 views
ADD COMMENT
0
Entering edit mode
@vegard-nygaard-6284
Last seen 19 months ago
Norway

Hi,

I suspect there are corrupt files and or bugs in the libraries.

 

However, I managed to import the data in R without errors by first downloading the two "matrix"-files from here:

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE13nnn/GSE13995/matrix/

And then import from file

set1 = getGEO(filename="GSE13995-GPL7752_series_matrix.txt.gz")
set2 = getGEO(filename="GSE13995-GPL7753_series_matrix.txt.gz")

I got some warnings but I think they can be ignored.

I dont think this will work from inside the GEO2R webinterface. You have to do it locally.

 

 

Vegard.

 

ADD COMMENT

Login before adding your answer.

Traffic: 290 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6