It would be great to have UPC support for Illumina arrays.

The illuminaHumanv4 package also has the hg19 locations in it;
'illuminaHumanv4GENOMICLOCATION'. So it sounds like you have everything you
need then.


On Fri, Nov 15, 2013 at 6:56 PM, Steve Piccolo <stephen.piccolo@hsc.utah.edu
> wrote:

> Hi Tim,
>
> Thanks for your message. Sorry for the delay in getting back to you.
>
> Several other people have also requested support for Illumina expression
> arrays. We are working to address this soon. However, rather than provide
> a function that is specific to Illumina arrays, we will likely provide a
> more generic UPC function that users can invoke for whatever platform they
> wish. Optionally, the user could indicate the GC content for each
> probe/gene on whichever platform they are using. So it sounds like this
> information could be extracted pretty easily from the illuminaHumanV.db
> packages, as Mark mentioned. I'm planning to work on this functionality
> soon and will add it to the devel version of the package. I'll let you
> know as soon as I have it ready for testing. I'll also see if I can put
> together a little primer that demonstrates how to invoke this on Illumina
> arrays specifically.
>
> As far as adding an option to specifically handle TCGA/RSEM files, can you
> give me a little more information about this file format. Is it mostly
> just used within TCGA? Or is it used more broadly in other contexts? I
> wouldn't be opposed to adding a helper function for handling these files,
> but am hesitant about opening this up for many different formats.
>
> Regards,
> -Steve
>
>
>
> Date: Fri, 15 Nov 2013 08:25:28 +0000
> From: Mark Dunning <mark.dunning@gmail.com>
> To: "Tim Triche, Jr." <ttriche@usc.edu>
> Cc: "bioconductor@r-project.org" <Bioconductor@r-project.org>
> Subject: Re: [BioC] SCAN.UPC for Illumina arrays?
> Message-ID:
>         <CAGpynukK721_7E52MbYgP=SLK1oKp=
> cww3-CfTyYsf-NCXwhtw@mail.gmail.com>
> Content-Type: text/plain
>
> Hi Tim,
>
> The probe sequences for illumina expression arrays are already available in
> the illuminaHumanV.db pacakges. e.g.
>
> illuminaHumanv4PROBESEQUENCE
>
> I'd be happy to add other fields if they would be useful for this kind of
> analysis.
>
> Best,
>
> Mark
>
>
> On Thu, Nov 14, 2013 at 10:38 PM, Tim Triche, Jr.
> <tim.triche@gmail.com>wrote:
>
> >I've been running arrays (Affy mouse, Affy human) and RNAseq data (also
> >mouse and human) through UPC() for the past few days, after seeing some
> >nice results from the PNAS paper in comparison to qPCR and fRMA.  However,
> >I was hoping that the same aspect of the method which makes it useful for
> >RNAseq (i.e., decoupling background/foreground estimation from
> >platform-parameter estimation) would allow me to use it on Illumina array
> >data.  Has anyone tried this?
> >
> >I can read in the appropriate bits (target sequence, length, GC content,
> >blah blah) for Illumina probes as if they were RNAseq data, or perhaps
> >assemble an oligo 'probedesign' package (less palatable) but I was hoping
> >someone else already bit the bullet.
> >
> >Also, I wrote some patches to make the package work better with e.g. TCGA
> >RSEM data, where the count files have an initial header line.  (Obviously
> >this was trivial, but there was another interesting opportunity for
> >improvement so I hit that too)  Would be interested to hear from the
> >authors/maintainers regarding its utility.
> >
> >Thanks,
> >--t
>
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