Problem with downloading GSE file by GEOquery

Question

[Kim]

Hello everyone

I'm learning to use GEOquery to analyze data from GEO. I can download GSM, GPL and GDS files from GEO with no problems, but I can't download GSE files.

The code I use: gse <- getGEO("GSE42657", destdir=".")

The returned message:

Error in open.connection(x, "rb") : 
  Timeout was reached: Connection timed out after 10015 milliseconds

Could you please tell me what happened and how to fix it?

Thank you very much

[Kim]

Thank Matthew. I've just tried your solution but using download.file command to download the file instead. Then I tried to open the file in R by getGEO but it's just running (nearly 1h already) without successfully opening the GSE file. Do you have any idea about this?

[Kim]

Everything is solved. I downloaded the file directly from the website and loaded it in R and now it works. Thank you very much for your solution.

[GenoMax]

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Answer 1

[MatthewP]

Hello, this may be connetion issue(happen often using GEOquery). One solution is download the Series Matrix File byhand. For example in your case

# download Matrix file
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42657/matrix/

# then in R
gse <- getGEO(filename="/yourpath/GSE42657_series_matrix.txt.gz", AnnotGPL=TRUE)