Question: Problem with downloading GSE file by GEOquery
gravatar for Kim
14 months ago by
Kim10 wrote:

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

ADD COMMENTlink modified 14 months ago • written 14 months ago by Kim10

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?

ADD REPLYlink written 14 months ago by Kim10

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.

ADD REPLYlink written 14 months ago by Kim10

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

ADD REPLYlink written 14 months ago by genomax89k
gravatar for MatthewP
14 months ago by
MatthewP710 wrote:

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

# then in R
gse <- getGEO(filename="/yourpath/GSE42657_series_matrix.txt.gz", AnnotGPL=TRUE)
ADD COMMENTlink written 14 months ago by MatthewP710
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