[BioC] Illumina Methylation. Normalization and statistics

Michael Walter michael.walter at med.uni-tuebingen.de
Wed Nov 19 16:18:35 CET 2008

Dear List,

We run our first slide of illumina's infinium methylation arrays. After searching the archive, I still have some general questions how to best analyze the data.

First of all, I'm would like to know some opinion on normalization. In my personal and probably simplistic view I'd think that normalization is not necessary since the value you get from the array is a ratio which is sample inherent (unlike a classical two-color expression array where you mix two samples to generate the expression ratio). Is this assumption correct or am I missing some important aspect?

Anyway, I'd like to perform background normalization which results as usual with illumina arrays in some negative values. Does anyone one have a neat solution for this problem or shall I just skip the probes?

Do I have to correct for some dye effect like for the golden gate methylation assay? Since the probes for methylated and unmethylated DNA incorporate the same dye this shouldn't be an issue? 

My final question is basically the most pressing: What kind of statistic test should I use? Since all the values are ratios between 0 and 1 I have a real bad feeling by simply running some t-tests. And if a t-test is the proper choice, shall I log-transform the data? 

Any input and shared experience with this type of array is highly appreciated.

Best Regards,

Dr. Michael Walter

The Microarray Facility
University of Tuebingen
Calwerstr. 7
72076  Tübingen/GERMANY

Tel.: +49 (0) 7071 29 83210
Fax. + 49 (0) 7071 29 5228

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