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

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?

geoquery
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written by Lunky • Lunky

please show your command, otherwise this is not reproducible

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written by ATpoint ATpoint

1 answer

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.

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written by Sean Davis Sean Davis

Thanks for the helpful answer Sean.

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written by Lunky • Lunky

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