Comments (2)
Hi,
Thanks for using the tool. This is a very interesting question but will require some extensive study.
Have you just tried to simply normalize the counts based on their copy numbers and perform the dchic?
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2256-5
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Thanks for the reply. I have used that methodology for CNV normalisation, but it works in conjunction with the iterative correction. So the resulting matrices are both ICE normalised and CNV normalized, and I thought for your methodology the input needed to be the raw matrices. If its ok to use ICE normalised matrices with dchic then I can give it a try.
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