Mat Algorithm Score For Chip Chip Data

Question

[kanwarjag]

I analysed Medip data with MAT algorithm and wonder how best should I be able to rank enrichment areas. Does higher MAT score means more enrichment or I should take lowest p values as the criteria.

Thanks

Answer 1

[Ying W]

Have a look at the MAT paper. It says that "MATscore which is a function of the intensity and the number of probes within a range of genomic sequence". Since you are interested in enrichment, ranking by p-values is probably best as long as there are not many ties, however, MATscore rank and p-values rank should be pretty similar.