Question: Error in Package GEOquery
0
gravatar for pankajnarula84
3.9 years ago by
India
pankajnarula8410 wrote:

Iam using 3.2.0 version of R on 64-bit system with Windows 7 OS. I am facing a problem while using the package GEOquery for bioinformatics

library(Biobase)
library(GEOquery)
library(limma)
library(RCurl)
library(XML)
getGEO("GSE1739", GSEMatrix = TRUE)  # to get the data

I got the error

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1739/matrix/
Error in function (type, msg, asError = TRUE)  :
Failed to connect to ftp.ncbi.nlm.nih.gov port 21: Timed out

Any help in this direction will be greatly appreciated. 

 

 

ADD COMMENTlink modified 2.2 years ago by mrmkanni930 • written 3.9 years ago by pankajnarula8410

This works for me. Can you access this via web browser?

Edit: As suggested on SO try GSEMatrix = FALSE

 

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by PoGibas4.7k

 Dear Pgibas, It works with (with some warnings) GSEMatrix = F. But when I run getGEOSuppFiles("GSE27447"). It throws an error

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27447/suppl/
No supplemental files found.
Check URL manually if in doubt
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27447/suppl/
NULL

How this can be handled? Is there any significant difference between setting GSEMatrix equal to TRUE or FALSE ?

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by pankajnarula8410

This is again likely the same connection problem as you noted in your original post.  You will likely want to use GSEMatrix=TRUE, but you can check the GEOquery vignette for details.  Yes, there is a significant difference between GSEMatrix=FALSE and and GSEMatrix=TRUE.  You will likely want to use GSEMatrix=TRUE, but you can check the GEOquery vignette for details.

ADD REPLYlink written 3.9 years ago by Sean Davis25k

Worked for me too, double check your connection

ADD REPLYlink written 3.9 years ago by andrew.j.skelton735.5k

Hi can any one please tell me how to install GEOquery packages on windows. It is showing an error XML file and RCURL file is not installed. Then I tried to install XML it is again showing error

ADD REPLYlink written 2.2 years ago by mrmkanni930
1

Please elaborate the exact error and versions of R and packages.

ADD REPLYlink written 2.2 years ago by pankajnarula8410
1

Please ask a new question adding a new post (link "New post" in the top-right side of your browser, or alternatively click here). Posting here is meant for adding answers to the current question (first post above).

ADD REPLYlink written 2.2 years ago by ddiez1.7k
1
gravatar for Hadiatashi
3.6 years ago by
Hadiatashi10
Hadiatashi10 wrote:

Hi Dear
Just type:

setInternet2(F)

then

getGEOSuppFiles("")

ADD COMMENTlink written 3.6 years ago by Hadiatashi10
0
gravatar for Sean Davis
3.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

This is a network connection problem, most likely because your firewall is not allowing port 21 connections.  You can check with your IT group to be sure.  If that is the case, ask if there is a way that you can set up a proxy to connect to NCBI ftp services.

ADD COMMENTlink written 3.9 years ago by Sean Davis25k

Dear Sean Davis, thanks for the reply. I turned off my firewall but problem is still persisting. 

ADD REPLYlink written 3.9 years ago by pankajnarula8410

You are most likely going to have to troubleshoot this problem with someone at your local institution.  Your issue seems to not be a problem with GEOquery but something specific to your setup.

ADD REPLYlink written 3.9 years ago by Sean Davis25k

I got the solution for the problem. I was setting proxy as Sys.setenv(http_proxy = "11.2.1.9:9090"). In addition I set FTP proxy as  Sys.setenv(ftp_proxy = "11.2.1.9:9090"). But now I am getting different error. 

gse <- getGEO("GSE1739",GSEMatrix=T)


ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1739/matrix/
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
line 2 did not have 6 elements

Here is session Info

 

sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] GEOquery_2.34.0      RCurl_1.95-4.6       bitops_1.0-6         BiocInstaller_1.18.2
[5] Biobase_2.28.0       BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
[1] tools_3.2.0  XML_3.98-1.1

 

 

 

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by pankajnarula8410

This works for me.  Again, the error message probably means that the file was not successfully downloaded.  I need to add some better checking on these errors, but here is what I get:

> gse = getGEO('GSE1739', GSEMatrix=TRUE)
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1739/matrix/
Found 1 file(s)
GSE1739_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1739/matrix/GSE1739_series_matrix.txt.gz'
ftp data connection made, file length 309166 bytes
opened URL
==================================================
downloaded 301 KB
....

Does your output (before the error message) show that the file (approximate size, 301 KB) was downloaded?  If not, then, perhaps try again later or double-check that you can connect to the NCBI ftp server correctly.

ADD REPLYlink written 3.9 years ago by Sean Davis25k
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: 2194 users visited in the last hour