[BioC] Bioconductor Digest, Vol 52, Issue 18

Simon Lin simonlin at duke.edu
Tue Jun 19 16:57:13 CEST 2007

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!


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
	<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?


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