Thank you very much.

Best regards,
Kaj


On Fri, Oct 4, 2013 at 8:03 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Kaj,
>
> Please don't take conversations off-list (e.g., use reply-all when
> responding).
>
> By org package, I mean something similar to the org.Hs.eg.db package, only
> for ovine instead of human. This is an organism level package, and only
> does annotations pertaining to IDs that are specific to that organism
> (based on Entrez Gene IDs, generally).
>
> Contrast that to a chip level package which maps chip IDs to various other
> annotations, letting you know for instance what gene's transcript is
> interrogated by a particular probe on the array.
>
> So, no you cannot use an org level package as annotation for a chip,
> because the org package doesn't know anything about the chip IDs. That is
> where the Agilent annotation file comes in. You can use that file to map
> the chip IDs to Entrez Gene IDs, and then it is simple to do further
> mapping on to other things you might care about (gene symbols, names, etc).
>
> But you won't be able to use things like nsFilter directly, as there isn't
> a chip-level package that maps chip IDs to other things. Instead you will
> have to 'roll your own' function.
>
> Best,
>
> Jim
>
>
>
>
> On Friday, October 04, 2013 1:00:07 AM, Kaj wrote:
>
>> On 04/10/13 03:23, James W. MacDonald wrote:
>>
>>> Hi Kaj,
>>>
>>> Currently you cannot create a chip level annotation package without a
>>> corresponding .db0 package. You can however create an organism level
>>> package using makeOrgPackageFromNCBI() in the AnnotationForge
>>> package, and then getting the annotation file from Agilent. You can
>>> then use the Entrez Gene IDs from the annotation file to then use
>>> select() to get whatever annotation you might want.
>>>
>>> If you are using limma, you can put the annotation data in the genes
>>> slot of the MArrayLM object, and those data will appear in your
>>> topTables().
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>
>>> On Thursday, October 03, 2013 6:21:22 AM, Kaj Chokeshaiusaha [guest]
>>> wrote:
>>>
>>>>
>>>> Dear R helper,
>>>>
>>>> I'm trying to create the annotation package for GPL10427. It is
>>>> ovine species platform, and there is no .db0
>>>> nor schema for it.
>>>>
>>>> I'm trying to read 'Creating an annotation package
>>>> with a new database schema'. It's ashamed of me, but I'm an R
>>>> beginner. I must accept that I loss most of the
>>>> important contents and I cannot gather enough ideas to apply it with
>>>> what I have to do.
>>>>
>>>> Would anyone please simplify me what I need to do in order to create
>>>> the platform in this situation?
>>>>
>>>> With Respects,
>>>> Kaj
>>>>
>>>>   -- output of sessionInfo():
>>>>
>>>> R version 3.0.2 (2013-09-25)
>>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>>
>>>> locale:
>>>>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>>>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>>>   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>>>>   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] parallel  stats     graphics  grDevices utils     datasets methods
>>>> [8] base
>>>>
>>>> other attached packages:
>>>> [1] hgu95av2.db_2.9.0     AnnotationForge_1.2.2 org.Hs.eg.db_2.9.0
>>>> [4] RSQLite_0.11.4        DBI_0.2-7 AnnotationDbi_1.22.6
>>>> [7] Biobase_2.20.1        BiocGenerics_0.6.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] IRanges_1.18.4 stats4_3.0.2   tcltk_3.0.2    tools_3.0.2
>>>>
>>>> --
>>>> Sent via the guest posting facility at bioconductor.org.
>>>>
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>>>> Search the archives:
>>>> http://news.gmane.org/gmane.**science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>>
>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>>
>> Dear Jim,
>>
>> Thank you very much for your answer. This can solve a lot of things.
>> Would you please clarify me a bit more about the 'Organism package'?
>>
>> I've processed an ExpressionSet object from raw data acquired from
>> this GPL10427 platform. I need to use some functions with the object;
>> for example, "nsFilter" in geneFilter package. These functions ask for
>> the annotation of the ExpressionSet to use all of their features.
>>
>> Can I set the 'Organism package' as the annotation of the ExpressionSet?
>>
>> Best Regards,
>> Kaj
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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