On Mon, Oct 5, 2009 at 11:35 AM, Kishor Tappita <kishor.tappita@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@gmail.com> wrote:
>> On Mon, Oct 5, 2009 at 9:03 AM, Kishor Tappita <kishor.tappita@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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