Hi Sir,

While running the somatic signature package,I am getting an error -

> sigs_nmf = identifySignatures(sca_mm, n_sigs, nmfDecomposition)
Error in rowQ(imat, ncol(imat)) : cannot handle missing values.
Calls: identifySignatures ... standardGeneric -> eval -> eval -> eval -> rowMax -> rowQ -> rowQ
In addition: Warning message:
In .local(x, rank, method, ...) :
  NMF residuals: final objective value is NA
Execution halted

Please have a look at the link https://www.dropbox.com/s/wc0a0sprzqcydnq/Data.maf?dl=0 , where a toy example of maf file is there and the following link for the code https://www.dropbox.com/s/m6pf05hnyfj7gos/code.R?dl=0

Swati

You likely may be running an outdated version of Bioconductor, based on the R version you reported. You should consider updating to the currently supported Bioconductor version, and hence of its packages. With the current version of SomaticSignatures, I cannot reproduce the error message that you report.

In your example, it seems that you have two defined 2 groups, but want to decompose the motif matrix into 5 signatures. Please note that the upper bound for the number of possible signatures is the minimum of the rows and columns of the motif matrix M, i.e. in your case 2 due to the 2 groups. This is by design of the underlying approach, and its matrix decomposition. You can have a look at the package vignette, and especially at the cited papers to learn about the background of this.