[BioC] GEOquery

[Sean Davis]

On Tue, Jul 8, 2008 at 11:09 AM, Harpreet Saini <hs1 at sanger.ac.uk> wrote:
> Hi Sean,
>
> Sorry to bother you again.
> But, I tried again many times, and still I am getting the same 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
>
> I use the following commands:
>>library(GEOquery)
>>gse4 <- getGEO("GSE4201", GSEMatrix = TRUE)

Thanks, Harpreet.  Could you send me the complete input and output?  I
cannot see what the output looks like to see if there is a problem
with download or what else might be the problem.

Sean

>
> Sean Davis wrote:
>>
>> 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
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>
> --
> Harpreet Kaur Saini
> Team 101, Room No. D313
> Wellcome Trust Sanger Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, CB10 1SA
> United Kingdom
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited,
> a charity registered in England with number 1021457 and a company registered
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>