[BioC] Creating Annotation package for GPL10427

[James W. MacDonald]

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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>>
>> --
>> 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