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Question: GEOquery http:// url error
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gravatar for jblack29
7 months 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

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

 

 

ADD COMMENTlink modified 7 months ago by SamGG90 • written 7 months ago by jblack290
0
gravatar for SamGG
7 months ago by
SamGG90
France
SamGG90 wrote:

Hi,

No error on my side. I was puzzled by the ftp protocol. In my case, the transfer used the https protocol to connect to the same server. Check if your Bioconductor installation is as new as as mine. My package are listed below.

Best.

 

> library(GEOquery)
> gset <- getGEO("GSE7696", GSEMatrix =TRUE)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7696/matrix/
OK
Found 1 file(s)
GSE7696_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7696/matrix/GSE7696_series_matrix.txt.gz'
Content type 'application/x-gzip' length 18131845 bytes (17.3 MB)
downloaded 17.3 MB

File stored at: 
C:\Users\XXXXXXXXXX\AppData\Local\Temp\RtmpUF0ZCn/GPL570.soft
Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :
  not all columns named in 'colClasses' exist
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GEOquery_2.40.0     Biobase_2.34.0      BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] httr_1.2.1           R6_2.2.0             BiocInstaller_1.24.0
[4] tools_3.3.2          RCurl_1.95-4.8       bitops_1.0-6        
[7] XML_3.98-1.5   
ADD COMMENTlink written 7 months ago by SamGG90
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