Error in Package GEOquery
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@pankajnarula84-7534
Last seen 6.4 years ago
India

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, proxy settings are OK.

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. 

 

 

geoquery error R microarray • 1.3k views
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Entering edit mode
@james-w-macdonald-5106
Last seen 2 hours ago
United States

The general recommendation in that situation is to try again later. Sometimes you just can't download right now.

> z <- getGEO("GSE1739")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1739/matrix/
Found 1 file(s)
GSE1739_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  301k  100  301k    0     0   176k      0  0:00:01  0:00:01 --:--:--  176k
File stored at:
/data3/tmp/Rtmp60L560/GPL201.soft
> z
$GSE1739_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 8793 features, 14 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM30361 GSM30362 ... GSM30374 (14 total)
  varLabels: title geo_accession ... data_row_count (21 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-r2-P1-cre-5_at (8793 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL201

And unfortunately all they have for this experiment are the MAS5.0 data, so you are stuck with that...

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