[BioC] problem with downloading dataset using GEOquery

Kishor Tappita kishor.tappita at gmail.com
Thu Oct 8 08:50:57 CEST 2009

Dear Sean,

Sorry for the delayed response. I was on leave yesterday. Thank you so
much for willing
to make the change.


On Tue, Oct 6, 2009 at 9:04 PM, Sean Davis <seandavi at gmail.com> wrote:
> On Mon, Oct 5, 2009 at 11:35 AM, Kishor Tappita <kishor.tappita at gmail.com>
> wrote:
>> Dear Sean,
>> Thank you so much for your reply and for letting me know the reason. I
>> will eagerly wait
>> for the GEO team to fix the problem.
> Thanks for the patience, Kishor.  Here is what the GEO team had to say:
> We do allow table-less Samples for tiling/promoter arrays. Some submitters
> do
> not generate normalized data for these types of Platforms. If processed data
> is available, we usually receive BED/BAR and TAS files which we link to the
> Sample record. In this particular case, the submitter supplied processed
> data
> on Series record GSE12864 (GSE12864 is part of superSeries GSE12885).
> So, I have made changes to GEOquery to deal with such GSEs, GPLs, and GSMs.
> These changes (version 2.9.6) will be available in the development branch in
> the next 1-2 days as the build system catches the changes.
> Sean
>> On Mon, Oct 5, 2009 at 6:46 PM, Sean Davis <seandavi at gmail.com> wrote:
>>> 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.
>>> Sean

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