Entering edit mode

4.9 years ago

sugus
▴
110

Hi there,

Briefly, I know NMF (non-negative matrix factorization) as modeling the matrix X of expression for g genes and s samples, constituting the product of a matrix G of g gene weights for k factors and a matrix S of s sample weights for k factors.

And I want to derive the matrix G for selecting genes with high weights for specific NMF factor (cluster). How to get this matrix in NMF()?

Thanks for someone could give me some hints.

Thank you so much. It's really helpful!

Hopefully you get the idea. But on reading again your question make sure that what you need is instead the H matrix of the transpose of the expression matrix.

If I have a new dataset with 30 different samples measured by the above 20 genes, how to project the new data into the low-dimensional subspace generated by NMF. Can I just multiplying the w matrix? Thanks in advance.

Hi Dario, I am wondering if it's possible to use an alternative distance except KL or euclidean in nmf() function? Thanks a lot!

Hi- looking at the documentation of

`nmf`

(i.e.`?nmf`

), it appears the parameter`method`

accept a keyword for the distance algorithm. Look at theAlgorithmsection of the docs for the available ones. E.g.`nmf(x, 2, method= 'lee')`