Hi team,

According to our microarray guru, the older arrays like U133 or mouse 430
do not have the ERCC probes, but some of the newer designs like Primeview
and maybe GeneST might have them.  Going forward, I think it's safe to
expect Affy to put the ERCC probes onto their new chips.

Jim, thanks again.  Do you know when the new package will be released into
the wild?  Would it be possible to get a beta version of it for our
in-house usage if it's a long ways off?

~Brian


On Tue, Jun 25, 2013 at 12:08 PM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote:

> 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@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@r-project.org [mailto:
> bioconductor-bounces@r-project.org] On Behalf Of James W. MacDonald
> Sent: Tuesday, June 25, 2013 16:26
> To: Brian J. Abraham
> Cc: Bioconductor@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@uw.edu
> > <mailto:jmacdon@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>.
> >
> >         _______________________________________________
> >         Bioconductor mailing list
> >         Bioconductor@r-project.org <mailto:Bioconductor@r-project.org>
> >         https://stat.ethz.ch/mailman/listinfo/bioconductor
> >         Search the archives:
> >
> > 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
>
> _______________________________________________
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>
>
>

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