使用生物信息R的GEOquery包的getGEO命令时出错

Question

Iam在Windows 7操作系统上使用3.1.2版本的R。我在使用用于生物信息学的软件包GEOquery时遇到了一个问题。

当我运行这些命令时

library(Biobase)
library(GEOquery)
library(limma)
library(RCurl)
library(XML)

# load series and platform data from GEO

gset <- getGEO("GSE1739", GSEMatrix = TRUE)

我得到了错误

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

但是，它可以与

gset <- getGEO("GSE1739", GSEMatrix = FALSE)

请帮帮我。提前谢谢。

Answer 1

超时错误可能是由网络问题引起的。如果仍然出现相同的错误，请检查您是否能够使用web浏览器访问ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1739/matrix/。在GEOquery版本2.32上，GSEMatrix = TRUE似乎可以正常工作。

#R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
#Copyright (C) 2014 The R Foundation for Statistical Computing
#Platform: x86_64-w64-mingw32/x64 (64-bit)
> library(GEOquery)
> 
> # load series and platform data from GEO
> # test GSEMatrix = TRUE
> gset <- 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'
using Synchronous WinInet calls
opened URL
downloaded 301 Kb

File stored at: 
C:\Users\david\AppData\Local\Temp\Rtmp8SU6Se/GPL201.soft

> summary(gset)
                             Length Class         Mode
GSE1739_series_matrix.txt.gz 1      ExpressionSet S4  
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
#...
other attached packages:
[1] GEOquery_2.32.0     Biobase_2.26.0      BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6   RCurl_1.95-4.5 tools_3.1.2    XML_3.98-1.1  
>