I am 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.
This works for me. Can you access this via web browser?
Edit: As suggested on SO try
GSEMatrix = FALSE
Dear Pgibas, It works with (with some warnings)
GSEMatrix = F. But when I run
getGEOSuppFiles("GSE27447"). It throws an error
How this can be handled? Is there any significant difference between setting
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=TRUE. You will likely want to use
GSEMatrix=TRUE, but you can check the GEOquery vignette for details.
Worked for me too, double check your connection
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
Please elaborate the exact error and versions of R and packages.
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