[BioC] GEOquery

[Sean Davis]

On Tue, Jul 8, 2008 at 12:00 AM, Harpreet Saini <hs1 at sanger.ac.uk> wrote:
> Hi Sean,
>
> Here is the output of sessionInfo()
>
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices datasets  utils     methods
> [8] base
>
> other attached packages:
> [1] GEOquery_2.4.0 RCurl_0.9-3    Biobase_2.0.1
>

Thanks, Harpreet.  That looks fine.  Was the download interrupted?  If
you could try it again and include the entire session (input and
output) if it fails, that might be helpful.

Sean

> "Sean Davis" <sdavis2 at mail.nih.gov> wrote:
>> On Mon, Jul 7, 2008 at 11:34 PM, Harpreet Saini <hs1 at sanger.ac.uk> wrote:
>> > Hi,
>> >
>> > I am trying to obtain GSE matrix files as expression sets by turning the GSEMatrix true as following:
>> >
>> >>gse<-getGEO("GSE2553", GSEMatrix = TRUE)
>> >
>> > I am getting the following error:
>> > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>> >  line 1 did not have 8 elements
>> > In addition: Warning messages:
>> > 1: In if (nchar(val) == nchar(x)) return(NA) :
>> >  the condition has length > 1 and only the first element will be used
>> > 2: In if (nchar(val) == nchar(x)) return(NA) :
>> >  the condition has length > 1 and only the first element will be used
>> >
>> > Any help?
>>
>> Thanks, Harpreet, for the report.  Could you send the output of
>> sessionInfo()?  On R-devel, I am not able to reproduce the error, so
>> it would help to have the further detail.
>>
>> Sean
>>
>>
>
>