Question: getGEO error fetching data
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19 months ago by
lallo_920
lallo_920 wrote:

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 • 277 views
modified 19 months ago by Vegard Nygaard110 • written 19 months ago by lallo_920
0
19 months ago by
Norway
Vegard Nygaard110 wrote:

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.