[BioC] ERCC spike-in probes in

[Hooiveld, Guido]

Hi,
Out of curiosity:
After reading this I just wondered whether the ERCC probes are unique for the primeview array, or are they also included in other Affymetrix array designs?
[In addition to the "standard" Dap, Thr, Phe and Lys -PolyA spikes I know of].

Thanks,
Guido

--------------------------------------------------------- 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:      guido.hooiveld at wur.nl
internet:   http://nutrigene.4t.com 
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010


-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of James W. MacDonald
Sent: Tuesday, June 25, 2013 16:26
To: Brian J. Abraham
Cc: Bioconductor at r-project.org
Subject: Re: [BioC] ERCC spike-in probes in

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

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