How to extract the result table from NMF clustering (R package 'NMF')?

Question

[yuezhao97]

Hi biostars,

I'm currently doing the analysis on my RNA-seq data of ~100 cancer samples and want to cluster them. I used the NMF clustering (run times = 200) and got a consensus cluster plot. Now I want to dig deeper into my results but can't find where to get the result table telling me which sample belong to which cluster. I'm wondering if anyone could help me with extracting the result table from the NMF clustering? Any information is appreciated. Many thanks!

Answer 1

[Jean-Karim Heriche]

For result <- nmf(...), the matrices are in result@fit@W and result@fit@H and can also be extracted with W <- basis(result) and H <- coef(result).

[yuezhao97]

Thank you, Jean-Karim Heriche, for your kind and useful information.

Just one more question, I ran the basis(result) and coef(result), and they gave me two matrices consisting of the values for genes and samples for clustering. Should I pick the largest value for each sample to determine the right cluster it belongs to?

[Jean-Karim Heriche]

NMF can be seen as a form of soft clustering in which the values can be interpreted as cluster membership "strength" or relevance. By picking the largest value, you're performing hard clustering, assigning items to only one cluster.

[yuezhao97]

OK I see. Thank you so much!