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promoter methylation data analysis - (Apr/22/2010 )

I am trying to analyze a promoter methylation data generated from Illumina I have beta values with loci for all my groups. I want to som basic stastical analysis like t test or other nonparemtric tests (ANOVA) and get differentially expressed loci. Have some one used matlab or R for this and any suggestion how to procede with this



I typed in MATLAB on the search engine and bumped on your post.

I am taking a matlab beginners' course and would like to know how you managed to use matlab on your methylation data. In our lab people use matlab to do image analysis only and was wondering how I can apply it to my methylation data. I used Rotor-Gene for a High Resolution Melt (HRM) analysis to determine percentages of methylation levels of my samples. Did you end up using matlab or did you find another way to deal with your data. I would be grateful if you could give me some advice.

Many thanks in advance,


I believe Illumina methylation analysis gives you high throughput data at single CpG site resolution, right? For such high throughput data, you really need to find someone who is skilled at bioinformatics and statistics to help you if you self have never done such analysis. Bioinformatics people use R package a lot for statistical analysis of such data.


If you want to analyse multiple CpG sites in one test its best to use mixed models to handle the correlation structure in the data (adjacent site may be highly correlated).

If you are new to statistics and genomics definetily consult with a statistician.