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

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.

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

getGEO(filename="GPL6480.soft")