[BioC] problems with readIllumina() for many BeadChips

[Ina Hoeschele]

Hi Mike et al.,
   first thanks for the help, I can now read and process the bead-level data from multiple (HumanHT-12 v4) Expression BeadChips just fine. Unfortunately I've run into the next hurdle, where I have a hard time finding information in the beadarray vignette or manual. The background corrected intensities in the txt files (expectedly) contain some negative values, but I can only find the log2 transformation. When I worked with the old version of beadarray a couple of years ago I used the background correction method of rma (backgroundMethod="normexp" in readIllumina) to obtain positive intensities prior to transformation, but this option seems no longer available? So how does beadarray deal with the negative intensities? Also, is there any opinion on the order of steps - transform bead-level intensities, then summarize, or summarize and then log2 transform, (either followed by normalization)?
Many thanks ... Ina


----- Original Message -----
From: "Mike Smith" <grimbough at gmail.com>
To: "Ina Hoeschele" <inah at vbi.vt.edu>
Cc: bioconductor at stat.math.ethz.ch
Sent: Thursday, February 17, 2011 1:59:11 PM
Subject: Re: [BioC] problems with readIllumina() for many BeadChips

Hi Ina,

Sorry, I think my message has probably created some confusion.

Version 2.0.4 is not the developmental version, its a patched version of the
release.  You can install it using biocLite("beadarray").  I uploaded the
patch yesterday, so it may take a day or so to filter through.

If you want to install the developmental version (currently 2.1.11) you
normally need to be running a developmental version of R, although there was
some discussion about this a few weeks back on this list.  This version
should be considered experimental and potentially buggy, but as you've seen
that can probably be applied to parts of the release package too!

Mike Smith
PhD Student
Computational Biology Group
Department of Oncology
Cambridge University
On 17 Feb 2011 16:52, "Ina Hoeschele" <inah at vbi.vt.edu> wrote: