Problem in getting geo file through GEOQUERY
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4 weeks ago
anasjamshed ▴ 120

I am using GEOquery package from bioconductor to download geoseries data:

library(GEOquery)
options(timeout = 600) # Set timeout to 10 minutes (600 seconds)
options(download.file.method.GEOquery = 'curl')
GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) #get the GEO object

But after running 5 times , it throws me the same error:

Found 2 file(s)
GSE1145-GPL570_series_matrix.txt.gz
Timeout was reached: [] Operation timed out after 120005 milliseconds with 3457024 out of 10863499 bytes receivedFile stored at:
C:\Users\Home\AppData\Local\Temp\RtmpaEE2lp/GSE1145-GPL570_series_matrix.txt.gz
Error in downloadFile(url, destfile = destfile, mode = "wb") : 
  Failed to download C:\Users\Home\AppData\Local\Temp\RtmpaEE2lp/GSE1145-GPL570_series_matrix.txt.gz!

What is the issue? Is there any problem with Geoquery package nowadays? I am using R-4.4.0 with Rstudio 2024.04.1

geoquery Geo • 422 views
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Query seems to be timing out. Try getting the file directly here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1145/matrix/GSE1145-GPL570_series_matrix.txt.gz

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I want to get lot of files through code

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It just runs fine for me with just a single line of code.

library(GEOquery)
GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE)

Found 2 file(s)
GSE1145-GPL570_series_matrix.txt.gz
Using locally cached version: /var/folders/sg/j7lq0tbs0vgcr488w32vc67h0000gq/T//RtmpRowoFH/GSE1145-GPL570_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
/var/folders/sg/j7lq0tbs0vgcr488w32vc67h0000gq/T//RtmpRowoFH/GPL570.soft.gz 
GSE1145-GPL8300_series_matrix.txt.gz
Using locally cached version: /var/folders/sg/j7lq0tbs0vgcr488w32vc67h0000gq/T//RtmpRowoFH/GSE1145-GPL8300_series_matrix.txt.gz
Using locally cached version of GPL8300 found here:
/var/folders/sg/j7lq0tbs0vgcr488w32vc67h0000gq/T//RtmpRowoFH/GPL8300.soft.gz 

GSE1145
$`GSE1145-GPL570_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 90 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM18422 GSM18423 ... GSM25854 (90 total)
  varLabels: title geo_accession ... relation (27 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL570 

$`GSE1145-GPL8300_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 12625 features, 17 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM25784 GSM25785 ... GSM25800 (17 total)
  varLabels: title geo_accession ... data_row_count (26 total)
  varMetadata: labelDescription
featureData
  featureNames: 1000_at 1001_at ... AFFX-YEL024w/RIP1_at (12625 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL8300 
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4 weeks ago
ATpoint 83k

Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If this all does not work maybe use GitPod (that has a good connection) or something like that to run the code, save as Rdata and then continue locally with that.

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Thanks . I have downloaded all other files but just have problem in

Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE) : 
  Failed to download C:\Users\Home\AppData\Local\Temp\Rtmp067S3j/GPL6244.soft.gz!

Can you send me ftp link so I can download that soft file manually?

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Can you send me ftp link so I can download that soft file manually?

Please find this link on your own by browsing the respective GEO entries. Biostars is not a service provider.

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