[BioC] problem with downloading dataset using GEOquery

Sean Davis seandavi at gmail.com
Mon Oct 5 15:16:37 CEST 2009

On Mon, Oct 5, 2009 at 9:03 AM, Kishor Tappita <kishor.tappita at gmail.com> wrote:
> Dear List,
> When I am trying to download  a dataset from GEO. I get the below
> error at the end of my
> command session.
>> dataset2 <- getGEO("GSE12885")
> File stored at: C:\DOCUME~1\WELCOM~1\LOCALS~1\Temp\RtmpYy3CGa/GPL5082.soft
> Error in txt[i] <- readLines(con, 1) : replacement has length zero

Hi, Kishor.  This is a problem with the GEO records for GPL5082.  In
particular, they are empty.  I don't know if GEO meant for this to be
so or not, but I was not aware that such empty records were acceptable
in GEO.  I'll follow up with the GEO staff to see what the deal is.


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