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.

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. > > _______________________________________________ > 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