[BioC] Bioconductor Digest, Vol 52, Issue 18

[Simon Lin]

We have evaluated the methods in Lumi using the MAQC benchmark data. The publication is under review. 

Pan, can you add the inter-lab concordance comparison results (Three curves: raw, Beadstudio, and lumi) in the lumi manual? Thanks!

Simon

================
Date: Tue, 19 Jun 2007 11:42:43 +0200
From: "daneel jordan" <daneel.robert at gmail.com>
Subject: [BioC] Illumina Treatment
To: bioconductor at stat.math.ethz.ch
Message-ID:
	<e88c6fe60706190242y1a0e8a22l7d91cddd854344a9 at mail.gmail.com>
Content-Type: text/plain

Dear Bioconductor user,


I need general help in illumina data treatments. I previously see that there
is Lumi packages to treat data, but I didn't see any benchmarch to compare
data normalization provided by lumi, and the ones from BeadStudio. (if you
have any can you provide any link?); with no benchmarks I would like to keep
the analysis as much standart as possible, using Rank-invariant from Bead
Studio. Unfortunately, as you may know for sure, this treatment create
negative values, because of bg subtraction, after log transformation, I have
NaN value, when I run a simple ttest analysis for each line of the array it
can happen that it complains for NAN values. what do you suggest?
add to the all chip a minim value in order to eliminate all possible
negative values?
threshold the data for negative values?
is there any way to tell the function t.test to not consider NaN fields?

Daneel

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