[BioC] About GEO submission of Illumina data

[Sean Davis]

Hi, Yu.

Your R version and the lumi version are both over 3 years old.  I'm
not sure that lumi even had the GEO submission stuff in it at that
time.  In any case, the best plan would be to upgrade to the newest R
and lumi and try again.

Sean


On Mon, Sep 12, 2011 at 9:08 PM, Yu Leng Phua <y.phua at imb.uq.edu.au> wrote:
> Hi Sean
>
> These are the required information
>
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils
>    datasets  methods
> [8] base
>
> other attached packages:
> [1] limma_2.14.7         lumi_1.6.3           mgcv_1.4-1
> [4] affy_1.18.2          preprocessCore_1.2.1 affyio_1.8.1
> [7] Biobase_2.0.1
>
>
>> produceGEOSampleInfoTemplate(lumi.example, lib.mapping = 'lumiMouseIDMapping',
> fileName = "GEOsampleInfo.txt")
> Error: could not find function
> "produceGEOSampleInfoTemplate"
>
>
> Thanks
> Yu
>
> On Mon, 12 Sep 2011 12:42:37 -0400
>  Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> Hi, Yu.
>>
>> Could you please include sessionInfo() and the code that
>>produces the error?
>>
>> Sean
>>
>>
>> On Sat, Sep 10, 2011 at 11:00 PM, Yu Leng Phua
>><y.phua at imb.uq.edu.au> wrote:
>>> Dear Pan
>>>
>>> How are you going? I am having some issues with my lumi
>>>package as I am
>>> unable to create the GEO template despite having the
>>>lumi library active.
>>> Error: could not find function
>>>"produceGEOSampleInfoTemplate"
>>>
>>> I would appreciate any help from you. Thanks!
>>>
>>> Cheers
>>> Yu
>>>
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>
>