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Question: nmf function not working
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gravatar for aslam.mohammed398
4 months ago by
aslam.mohammed3980 wrote:
When I use identifySignatures from somaticsignatures package it throws me out this error. What do I need to change ?
identifySignatures(sca_mm,5,nmfDecomposition)
Error in (new("standardGeneric", .Data = function (x)  : 
  unused arguments (model = list("NMFstd", 5, 0), method = "random")
ADD COMMENTlink modified 9 days ago by Xin0 • written 4 months ago by aslam.mohammed3980

Please read the posting guide and provide the required details.

ADD REPLYlink written 4 months ago by Julian Gehring1.3k

Hi, Aslam

I have encountered an exactly same problem. My code was working but I recently updated NMF packages (following biocLite suggestion). Then, when I ran the command, I had the error:

sigs_nmf = identifySignatures(sca_mm, n_sigs, nmfDecomposition)
Error in (new("standardGeneric", .Data = function (x)  : 
  unused arguments (model = list("NMFstd", 5, 0), method = "random")

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Version of pacakges:

NMF_0.21.0

SomaticSignatures_2.16.0

VariantAnnotation_1.26.1 

ADD REPLYlink written 3 months ago by li110

Thank you for the report. I have not been able to reproduce this issue with the same package versions as you have. Could you please post a complete example that I can rerun (from the starting of the R session until the error occurs) together with a complete output of the sessionInfo command?

ADD REPLYlink written 3 months ago by Julian Gehring1.3k
0
gravatar for Xin
9 days ago by
Xin0
Xin0 wrote:

Hi Aslam,

I guess there should be some unknown library conflicts. Detaching and reloading NMF package may work.

ADD COMMENTlink written 9 days ago by Xin0
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