[BioC] Analysis of Omni Express / Omni Express FFPE chips

[Valerie Obenchain]

Hi Ed,

A Bioc package has been submitted that contains qa functions for FFPE 
data. The package is not yet approved but I've cc'd the author (Levi) on 
this message. He may have some helpful suggestions of how he has dealt 
with these data.

Valerie

On 12/19/2011 04:03 AM, Ed Schwalbe [guest] wrote:
> Dear list,
>
> I've just come into possession of some pilot study data run on Illumina's Omni Express and Omni Express FFPE SNP array platforms.
>
> I was wondering whether I could process these data within BioConductor, and if so, which packages might be suitable. I've had a look around the packages repository, and haven't yet found a perfect match for what I want to do (which is the standard normalisation and segmentation). It is also possible that the chips are new enough that annotation packages do not exist for them yet.
>
> I'd be grateful for any guidance you could offer.
>
> Best wishes,
>
> Ed
>
>   -- output of sessionInfo():
>
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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