[BioC] SCAN.UPC for Illumina arrays?

[Steve Piccolo]

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 at gmail.com>
To: "Tim Triche, Jr." <ttriche at usc.edu>
Cc: "bioconductor at r-project.org" <Bioconductor at r-project.org>
Subject: Re: [BioC] SCAN.UPC for Illumina arrays?
Message-ID:
	<CAGpynukK721_7E52MbYgP=SLK1oKp=cww3-CfTyYsf-NCXwhtw at 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 at 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