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Question: Error in GEOquery
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gravatar for rk489
7 months ago by
rk4890
United Kingdom
rk4890 wrote:

Hi, I'm trying to download RNAseq data from the GEO dataset "GSE67835". However, I'm getting the following error: 

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=GPL15520&form=text&view=full' 

Here's the code:

> library(GEOquery)

> eset = getGEO("GSE67835")
Found 2 file(s)
GSE67835-GPL15520_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67835/matrix/GSE67835-GPL15520_series_matrix.txt.gz'
ftp data connection made, file length 9612 bytes
opened URL
==================================================
downloaded 9612 bytes

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=GPL15520&form=text&view=full'

I've also tried changing the download.file option: options('download.file.method.GEOquery' = 'curl') but that is still giving the following error - 

Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument

> options('download.file.method.GEOquery' = 'curl')
> eset = getGEO("GSE67835")
Found 2 file(s)
GSE67835-GPL15520_series_matrix.txt.gz
Using locally cached version: /var/folders/db/c2n7rjq5587dp9vzs9zmqd600000gn/T//RtmpcXc3q8/GSE67835-GPL15520_series_matrix.txt.gz
Using locally cached version of GPL15520 found here:
/var/folders/db/c2n7rjq5587dp9vzs9zmqd600000gn/T//RtmpcXc3q8/GPL15520.soft 
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument

Following is the sessionInfo:

>sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] GEOquery_2.28.0    Biobase_2.22.0     BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] bitops_1.0-6   RCurl_1.95-4.5 tools_3.0.3    XML_3.95-0.2  

 

I would appreciate if you could tell me where the mistake is. Thanks!

ADD COMMENTlink modified 7 months ago by James W. MacDonald45k • written 7 months ago by rk4890

Why don't you donwload it manually by searching your gse id and then download raw data by clicking http , download soft files and matrix file as well .

other than that try this code may be this work for you.

this is the method for downloading soft files:

library(GEOquery)

gse <- getGEO('GSE67835',GSEMatrix=TRUE)

pheno.df <- pData(phenoData(gse[[1]]))

pData(gse[[1]])

 

 

ADD REPLYlink written 7 months ago by nia0
0
gravatar for James W. MacDonald
7 months ago by
United States
James W. MacDonald45k wrote:

If you look at the page you are trying to download from, the raw sequencing files are at the SRA, and the only other available data are csv files, neither of which will be downloaded by getGEO (what you do get are the MAIME data describing the experiment, which is probably useful by itself).

If you want the raw counts, you can use getGEOSuppFiles:

> eset = getGEOSuppFiles("GSE67835")
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67835/suppl/
OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67835/suppl//GSE67835_RAW.tar'
Content type 'application/x-tar' length 32163840 bytes (30.7 MB)
downloaded 30.7 MB

Or if you want the FASTQ files, you need to go to the SRA and learn about how to download and convert their .sra files.

ADD COMMENTlink written 7 months ago by James W. MacDonald45k
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