[BioC] ERCC spike-in probes in

[James W. MacDonald]

Hi Brian,

I am not going to build this package for the current version of 
Bioconductor, but it will appear in the next release. Please note that I 
have replaced the 'stock' Affymetrix cdf with this one, so people will 
automatically get the cdf that contains the ERCC probe mappings (e.g., 
this cdf package will be called 'primeviewcdf', just like the current 
one, but will contain the ERCC probes as well).

Best,

Jim



On 6/24/2013 6:26 PM, Brian J. Abraham wrote:
> Hi Jim,
>
> The CDF is publicly available via GEO.  If this doesn't work, I can 
> find another way to get it to you.  Thanks for taking this on!
>
> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16043
>
> ~Brian J. Abraham
> Postdoctoral Associate
> Lab of Richard Young
> Whitehead Institute for Biomedical Research
> Nine Cambridge Center
> Cambridge, MA 02142
>
>
> On Mon, Jun 24, 2013 at 5:14 PM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     Hi Brian,
>
>     Sure. You can send it directly to me.
>
>     Best,
>
>     Jim
>
>
>
>
>     On 6/24/2013 3:33 PM, Brian Abraham [guest] wrote:
>
>         Hi team,
>
>         I'm part of the lab that made everyone's microarray analysis
>         more difficult by demanding everyone do ERCC spike-in
>         normalization.  Unfortunately, the primeviewcdf does not
>         automatically contain the probeset IDs for ERCCs, despite the
>         probes being physically on the chip.  We've worked with Affy
>         to get a custom cdf made that contains the locations of the
>         ERCC probes on the primeview chip.  Would you be interested in
>         folding this into your code so that more people can benefit
>         from it?
>
>           -- output of sessionInfo():
>
>             sessionInfo()
>
>         R version 3.0.1 (2013-05-16)
>         Platform: x86_64-pc-linux-gnu (64-bit)
>
>         locale:
>           [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>           [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>           [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>           [7] LC_PAPER=C                 LC_NAME=C
>           [9] LC_ADDRESS=C               LC_TELEPHONE=C
>         [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>         attached base packages:
>         [1] parallel  stats     graphics  grDevices utils     datasets
>          methods
>         [8] base
>
>         other attached packages:
>         [1] makecdfenv_1.36.0  affyio_1.28.0      affy_1.38.1      
>          Biobase_2.20.0
>         [5] BiocGenerics_0.6.0
>
>         loaded via a namespace (and not attached):
>         [1] BiocInstaller_1.10.2  preprocessCore_1.22.0 tools_3.0.1
>         [4] zlibbioc_1.6.0
>
>         --
>         Sent via the guest posting facility at bioconductor.org
>         <http://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
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099