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I am starting analysis of metabolomics data.

I want to use R only for the statistical analysis of the raw matrix: I mean normalization, pca , clustering, missing value imputation anova ....

As I first approach since I am coming from microarray I am thinking to produce an expressionset and use my scripts for the arrays.

Any suggestion? I have seen the metabolomics packages in bioconductor and I am not so enthusiastic but maybe I have to spend more time learning about them.

Thanks for any suggestion

I'm actually at the same point right now, starting with metabolomics data and coming from microarrays/RNAseq... I think it is worthwhile spending a little more time with the packages and to learn all classes etc before implementing something new.

cheers, jo