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
