Thanks for your message. Sorry for the delay in getting back to you.
Several other people have also requested support for Illumina
arrays. We are working to address this soon. However, rather than
a function that is specific to Illumina arrays, we will likely provide
more generic UPC function that users can invoke for whatever platform
wish. Optionally, the user could indicate the GC content for each
probe/gene on whichever platform they are using. So it sounds like
information could be extracted pretty easily from the
packages, as Mark mentioned. I'm planning to work on this
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
together a little primer that demonstrates how to invoke this on
As far as adding an option to specifically handle TCGA/RSEM files, can
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
but am hesitant about opening this up for many different formats.
Date: Fri, 15 Nov 2013 08:25:28 +0000
From: Mark Dunning <firstname.lastname@example.org>
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?
<cagpynukk721_7e52mbygp=slk1okp=cww3-cftyysf-ncxwhtw at="" mail.gmail.com="">
The probe sequences for illumina expression arrays are already
the illuminaHumanV.db pacakges. e.g.
I'd be happy to add other fields if they would be useful for this kind
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
>mouse and human) through UPC() for the past few days, after seeing
>nice results from the PNAS paper in comparison to qPCR and fRMA.
>I was hoping that the same aspect of the method which makes it useful
>RNAseq (i.e., decoupling background/foreground estimation from
>platform-parameter estimation) would allow me to use it on Illumina
>data. Has anyone tried this?
>I can read in the appropriate bits (target sequence, length, GC
>blah blah) for Illumina probes as if they were RNAseq data, or
>assemble an oligo 'probedesign' package (less palatable) but I was
>someone else already bit the bullet.
>Also, I wrote some patches to make the package work better with e.g.
>RSEM data, where the count files have an initial header line.
>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.