Originally posted by simonandrews
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another question would be the normalization for the ChIP-seq counts. Seqmonk provides two ways to normalize them.
1. log2 CPM
2. largest data set
my understanding is that normalizing to the largest data set is essentially the same as
log2 CPM but scale up with some factor.
the problem with log2 CPM normalization is that you got some negative values.
Does it still make sense if I use result from the log2 CPM to do the downstream analysis like scatter plot and hierachical cluster? Thanks!
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