getGEO function not identifying local file
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1
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Prasanth ▴ 20
@psambhu-8099
Last seen 4 months ago
India

Hello there, I am using Windows 10 machine. Trying to get GEO files using getGEO function. Since the internet is sporadic in my part of the world, I always try to download files separately and call it through R-console. But I couldn't get the GEO files using getGEO() function. I searched the support website and found to directly link the soft file.

> getGEO("GPL6480.soft")
# Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument

Could you please tell me what did I do wrong. What is the correct way to link my already downloaded soft file from the directory folder?

Many thanks.

prasanth

geoquery getGEO • 1.8k views
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Prasanth ▴ 20
@psambhu-8099
Last seen 4 months ago
India

Thanks. I tried that at first. It didn't come up. Then I cleaned all the files from the "temp" folder. And restarted R console. Then it sourced from the R wd. And it worked.

 

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@sean-davis-490
Last seen 14 days ago
United States

I think you'll need to specify the filename explicitly:

getGEO(filename="GPL6480.soft")
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In my case, the

getGEO(filename="GSE11724.soft")

give the following error

Error in readLines(con, lineCounts[1, 1] - 1) : invalid 'n' argument
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0
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Make sure that the file exists, that the download completed (the file size should be bigger than 0, at least), and that you are specifying the path to the file correctly.

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