[BioC] ERCC spike-in probes in

[James W. MacDonald]

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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at 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