Ok I guess I'm a bit dense, but bear with me here.  I have used crlmm in
the past on SNP6 arrays, but not on HuEx arrays (yet).

oligo and oligoClasses are both used by packages like crlmm, charm, etc.
where the locations of interrogated sequences are very important.  So the
pdInfo packages do (ought to?) have information about what probesets
interrogate what subsequences along an overall transcript or genomic region
(typically this will be complete with strand, though not always).   What
would be involved in taking the above information and turning it into a
GRanges/GRangesList suitable for mapping large sparse Matrix objects?

Just wondering.  For 3' arrays, many SNP arrays, and DNA methylation
arrays, the process is fairly trivial (i.e. "I needed to resolve the
problem so I wrote code to coerce GEO data into the appropriate
container").  Is there a general overarching logic that could be harnessed
to dump existing results into memory-efficient data structures of the sort
now available through GenomicRanges (and SEs)?

In particular, for the HuEx arrays, it just dawned on me that a GRangesList
of probesets and transcript mappings could be really handy.

How onerous of a task would this, in your (James') estimation, be?



On Fri, Dec 14, 2012 at 6:58 AM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Please don't take conversations off-list. We like to think of the list
> archives as a repository of information.
>
> On 12/14/2012 5:45 AM, Bruno Giotti wrote:
>
>> Ok thanks, but what should i do to query the pd.hugene.1.1.st.v1
>> annotation pack and retrieving some useful IDs? I could use the package you
>> suggested me but i'd like to first understand how to use this one (
>> pd.hugene.1.1.st.v1).
>>
>
> The pd.hugene.1.1.st.v1 package is NOT an annotation package. Instead, it
> maps the locations of probes on the array to different probesets. This
> package is used by oligo to decide which probes go into which probeset, so
> you can summarize at different levels (e.g., for the HuGene arrays, at the
> 'probeset' level, which is roughly exon-level, or at the transcript level).
>
> Unless you have a real need to know where things are on the chip, the
> pd.hugene.1.1.st.v1 package is not of much use. Well, let me take that
> back. I have found that the intronic background controls have a really bad
> habit of popping up in lists of differentially expressed genes. There are
> any number of hypotheses that I can come up with that would explain why
> this is so, but in the end I haven't found any end users who really care.
> So I use the pd.hugene.1.1.st.v1 package to figure out which probesets are
> not controls, and exclude them prior to selecting differentially expressed
> genes. The getMainProbes() function in affycoretools is useful in this
> respect.
>
> So back to the story at hand. Since the pd.hugene.1.1.st.v1 package
> doesn't do annotations, you need to use the hugene11sttranscriptcluster.db
> package. It does use a SQLite database as its backend, but unless you like
> to do SQL queries this is of no relevance.
>
> The canonical reference for using these annotation packages is the Intro
> to Annotation Packages, which can be accessed by
>
> library(**hugene11sttranscriptcluster.**db)
> openVignette()
>
> and then choosing
>
>  AnnotationDbi - AnnotationDbi: Introduction To Bioconductor Annotation
> Packages
>
> if you care about the internals, you can read
>
> AnnotationDbi - How to use bimaps from the ".db" annotation packages
>
> And if you just want to create annotated output, take a look at the
> annaffy package, which automates these things.
>
> Best,
>
> Jim
>
>
>  Thaniks again
>>
>> > Date: Thu, 13 Dec 2012 11:53:52 -0500
>> > From: jmacdon@uw.edu
>> > To: guest@bioconductor.org
>> > CC: bioconductor@r-project.org; latini18@hotmail.com;
>> Benilton.Carvalho@cancer.org.**uk <Benilton.Carvalho@cancer.org.uk>
>> > Subject: Re: [BioC] Oligo package annotation
>>
>> >
>> >
>> >
>> > On 12/13/2012 11:48 AM, Bruno [guest] wrote:
>> > > Hi all,
>> > > My question is quite straight-forward: how do i retrieve EntrezId or
>> geneSymbol for pd.hugene.1.1.st.v1 to merge into my gene expression matrix?
>> I havent found any vignettes explaining this. I know that the annotation
>> file is a SQLite DB which i have to query. However im failing to find the
>> tables i need. Sorry if i persevere in not explaining myself enough.
>> >
>> > It depends on what level you used for summarization. Assuming that you
>> > used transcript-level summarization (which I would highly recommend),
>> > you want to use the hugene11sttranscriptcluster.db package. If you did
>> > something like
>> >
>> > rma(<filename>, target="probeset")
>> >
>> > then you want the hugene11stprobeset.db
>> >
>> > Best,
>> >
>> > Jim
>> >
>> >
>> > >
>> > >
>> > > -- output of sessionInfo():
>> > >
>> > > R version 2.15.1 (2012-06-22)
>> > > Platform: x86_64-pc-mingw32/x64 (64-bit)
>> > >
>> > > locale:
>> > > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
>> > > [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
>> > >
>> > > attached base packages:
>> > > [1] stats graphics grDevices utils datasets methods base
>> > >
>> > > other attached packages:
>> > > [1] pd.hugene.1.1.st.v1_3.8.0 oligo_1.22.0 affyPLM_1.34.0
>> preprocessCore_1.20.0 latticeExtra_0.6-24
>> > > [6] lattice_0.20-10 RColorBrewer_1.0-5 BiocInstaller_1.8.3
>> simpleaffy_2.34.0 gcrma_2.30.0
>> > > [11] genefilter_1.40.0 affy_1.36.0 limma_3.14.3 RSQLite_0.11.2
>> DBI_0.2-5
>> > > [16] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0
>> > >
>> > > loaded via a namespace (and not attached):
>> > > Error in x[["Version"]] : subscript out of bounds
>> > > In addition: Warning message:
>> > > In FUN(c("affxparser", "affyio", "annotate", "AnnotationDbi",
>> "Biostrings", :
>> > > DESCRIPTION file of package 'survival' is missing or broken
>> > >
>> > > --
>> > > Sent via the guest posting facility at bioconductor.org.
>> > >
>> > > ______________________________**_________________
>> > > Bioconductor mailing list
>> > > Bioconductor@r-project.org
>> > > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> > > 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
>> >
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
> ______________________________**_________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
> Search the archives: http://news.gmane.org/gmane.**
> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

	[[alternative HTML version deleted]]

