For GEOquery, do I need to convert my GPL file from .txt to .soft?

Question

[Lunky]

I received the following error message but was able to click the link to download the GPL file:

Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : download from 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL13534&form=text&view=full' failed

However, it is in .txt format instead of .soft. I'm not familiar with the .soft format, do I need to convert it somehow?

[ATpoint]

please show your command, otherwise this is not reproducible

Answer 1

[Sean Davis]

I suspect that the error you are seeing is an intermittent network error or has to do with a data refresh at NCBI where GEO is hosted. Retrying will likely solve your issue. I was able to perform the following without a problem:

library(GEOquery)
getGEO('GPL13534')

To answer your question directly, the file suffix is .txt but the file format is SOFT format; no conversion is needed.

If you still have problems, in rare cases where you are accessing the file from a browser just fine but R (or the command line) produce errors, there may be a proxy setting to tinker with, but I suspect you'd see problems in other areas and not just GEOquery with this specific GPL.

[Lunky]

Thanks for the helpful answer Sean.