Question: GEOquery R Package Error: cannot open URL (http://)
0
gravatar for jblack29
3.5 years ago by
jblack290
jblack290 wrote:

Hey there, I'm hoping someone can help me with an error I just can't seem to solve. I'm also fairly new to using R and associated packages so please bear with me.

I'm using limma and GEOquery to download a dataset (accession GSE7696) to gain a gene expression list for further use. GEOquery is able to find this dataset and will download the initial GSE7696_series_matrix.txt.gz file through an ftp url with no issues. It then gets to the next url with begins with http and throws an error that it cannot open the url. Opening the url automatically downloads a txt file of information regarding the affymatrix chip used etc. I've pasted my code and errors below. Any help that can be provided would be massively appreciated!! (also additional info, using a linux machine)

Code

library(Biobase) library(GEOquery) library(limma) gset <- getGEO("${SERIES_ACCESSION}", GSEMatrix =TRUE)

Error Message - at very bottom

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

plotMA

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7696/matrix/
Found 1 file(s)
GSE7696_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7696/matrix/GSE7696_series_matrix.txt.gz'
ftp data connection made, file length 18131845 bytes
==================================================
downloaded 17.3 MB

Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full'
Calls: getGEO ... parseGSEMatrix -> getGEO -> getGEOfile -> download.file
Execution halted
...Done
error microarray analysis R geo • 2.2k views
ADD COMMENTlink modified 3.5 years ago by Santosh Anand5.2k • written 3.5 years ago by jblack290
0
gravatar for Santosh Anand
3.5 years ago by
Santosh Anand5.2k
Santosh Anand5.2k wrote:

cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full'

This query is "GPL570", which is not an Expression Matrix. This is one of the Affy platforms for doing microarray. See https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570

[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

That said, check your query accession numbers. If you like to parse them as expression matrix, they should start like GSE...

ADD COMMENTlink written 3.5 years ago by Santosh Anand5.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 820 users visited in the last hour