9.9 years ago by
University of Manchester, UK
I have always found the biggest problem of comparing ChIP-chip/seq binding regions with expression data is the use of gene symbols, i.e. whether the genes associated with binding regions also represented in the gene expression data (and visa versa).
So you could simply try intersecting ChIP-chip binding region coordinates (+/-) a threshold of your choice (say 50 or 100kb) with the probeset coordinates from the gene expression data.
For a more in depth and modelled approach i would follow Casey's suggestion.
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9.9 years ago by
Ian ♦ 5.7k