[BioC] Illumina Treatment

Mark Dunning md392 at cam.ac.uk
Wed Jun 20 19:45:18 CEST 2007

Hi Daneel,

To my knowledge there are is no suitable benchmark dataset available
through Bioconductor for comparing methods.

In our experience, we find the method of normalisation implemented in
BeadStudio is not helpful if you want to analyse data on the log-scale
using the tools available in Bioconductor. This is because of the huge
number of NA values that are produced and large increase in variability
at low intensities.

I would recommend exporting non-normalised data fromn BeadStudio and
then normalising using traditional methods such as quantile after a log2
transformation or using the VST method of lumi.



On Tue, 2007-06-19 at 11:42 +0200, daneel jordan wrote:
> 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
> 	[[alternative HTML version deleted]]
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