Question: Regarding Somatic Mutation Signature
0
gravatar for sj1
3.0 years ago by
sj110
sj110 wrote:

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

ADD COMMENTlink modified 3.0 years ago by Julian Gehring1.3k • written 3.0 years ago by sj110

What is the output of your sessionInfo?

ADD REPLYlink written 3.0 years ago by Julian Gehring1.3k

This is the required output of sessioninfo -

> sessionInfo()

R version 3.2.4 (2016-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN       
 [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSAGES=en_IN   
 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Swati

ADD REPLYlink written 3.0 years ago by sj110
Answer: Regarding Somatic Mutation Signature
0
gravatar for Julian Gehring
3.0 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:

You likely may be running an outdated version of Bioconductor, based on the R version you reported.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.

 

ADD COMMENTlink written 3.0 years ago by Julian Gehring1.3k
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