[BioC] Oligo package: paCalls question

[James W. MacDonald]

HI Alison,

When you do paCalls with method = "PSDABG", you are getting P/A calls at
the 'probeset' level (which in Affymetrix terms is the probe set region or
PSR, which roughly corresponds to exon-level). But when you do rma with
target = "core", you are summarizing data at the 'core' or transcript level
(e.g., at this level all the PSRs that interrogate a given gene are
summarized together).

So you cannot use oligo to generate P/A calls at the transcript level. It's
my understanding that you can do this with xps, but I am unfamiliar with
that package. However, a quick search of the BioC list using 'stratowa
pacalls' got as the first hit this message:
https://stat.ethz.ch/pipermail/bioconductor/2014-August/060977.html

Best,

Jim


On Thu, Sep 4, 2014 at 1:36 PM, Alison Ziesel <aziesel at emory.edu> wrote:

> Hello all,
>
> I’ve got very basic familiarity with the oligo package, but I’ve ran into
> a bit of trouble with the paCalls function. I’d like to restrict the probes
> in my eSet object to only those called present. Here’s what I’ve done thus
> far:
>
> >library(“oligo”)
> >library("pd.hugene.2.0.st”)
> >allchips <- read.celfiles(“my list of cel files”)
>
> >allchipspa <-paCalls(allchips, method=“PSDABG”, verbose=TRUE)
> >present <- rownames(allchipspa)
> >allchips_present <- exprs(allchips[present,])
>
> Error in exprs(allchips[present, ]) :
>   error in evaluating the argument 'object' in selecting a method for
> function 'exprs': Error in orig[[nm]][i, , ..., drop = drop] : subscript
> out of bounds
>
> Clearly my last line doesn’t do what I want it to do: filter the object
> allchips versus the list of present probes in the object present. I suppose
> at this point I should also confirm that my object allchipspa is just the
> present probes!  What’s the correct way to perform this filter step? I’d be
> grateful for any insight you may have.
>
> > sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-apple-darwin13.1.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>  base
>
> other attached packages:
>  [1] pd.hugene.2.0.st_3.8.1 RSQLite_0.11.4         DBI_0.2-7
> oligo_1.28.2
>  [5] Biostrings_2.32.1      XVector_0.4.0          IRanges_1.22.10
> Biobase_2.24.0
>  [9] oligoClasses_1.26.0    BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.36.0     affyio_1.32.0         BiocInstaller_1.14.2
> bit_1.1-12
>  [5] codetools_0.2-8       ff_2.2-13             foreach_1.4.2
>  GenomeInfoDb_1.0.2
>  [9] GenomicRanges_1.16.4  iterators_1.0.7       preprocessCore_1.26.1
> splines_3.1.1
> [13] stats4_3.1.1          tools_3.1.1           zlibbioc_1.10.0
>
> alison
>
> Alison Ziesel
> Department of Ophthalmology, Emory University
> aziesel at emory.edu
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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

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