error using deconvolution_nmf

[Sames-Jtudd]

Hi, Im having some issues with the above command. Hope you can help. Any ideas you had would be very useful.

When running the following command

denovo_signatures <- deconvolution_nmf(input_data = propMutsByCat, type = "SNV", range_of_sigs = 2:10 ,nrun = 20 ,method = "brunet" ,resdir = resdir) I get the following output

[1] "Estimating the optimal number of mutational signatures..." Timing stopped at: 1.475 2.602 4.144 Timing stopped at: 1.68 2.829 4.582 Timing stopped at: 1.478 2.621 4.167 Timing stopped at: 1.651 2.82 4.545 Timing stopped at: 1.477 2.622 4.166 Timing stopped at: 1.666 2.826 4.565 Timing stopped at: 1.497 2.586 4.206 Timing stopped at: 1.656 2.74 4.471 Timing stopped at: 1.478 2.668 4.21 Error in (function (...) : All the runs produced an error: -#1 [r=2] -> NMF::nmf - 20/20 fit(s) threw an error.

Error(s) thrown:

• run #1: unused arguments (model = list("NMFstd", 2, 0), method = "random") -#2 [r=3] -> NMF::nmf - 20/20 fit(s) threw an error.

Error(s) thrown:

• run #1: unused arguments (model = list("NMFstd", 3, 0), method = "random") -#3 [r=4] -> NMF::nmf - 20/20 fit(s) threw an error.

Error(s) thrown:

• run #1: unused arguments (model = list("NMFstd", 4, 0), method = "random") -#4 [r=5] -> NMF::nmf - 20/20 fit(s) threw an error.

Error(s) thrown:

• run #1: unused arguments (model = list("NMFstd", 5, 0), method = "random") -#5 [r=6] -> NMF::nmf - 20/20 fit(s) threw an error.

Error(s) thrown:

• run #1: unused arguments (model = list("NMFstd", 6, 0), method = "random") -#6 [r=7] -> NMF::nmf - 20/20 fit(s) threw an error.

Error(s) thrown:

• run #1: unused arguments (model = list("NMFstd", 7, 0), method = "random") -#7 [r=8] -> NMF::nmf - 20/20 fit(s) threw an

given that the input data is generated using a Palimpsest command Im surprised that this threw an error.

hear is a sample of the input file

head(propMutsByCat) Sample1 Sample2 Sample3 Sample4 Sample5 CA_A.A 0.025848142 0.017460317 0.019760790 0.017004578 0.0192307692 CA_A.C 0.011308562 0.015873016 0.014040562 0.015042511 0.0142679901 CA_A.G 0.001615509 0.003174603 0.003120125 0.002616089 0.0006203474 CA_A.T 0.016962843 0.012698413 0.010400416 0.012426422 0.0130272953 CA_C.A 0.016962843 0.017460317 0.015600624 0.017004578 0.0136476427 CA_C.C 0.010500808 0.012698413 0.011960478 0.010464356 0.0068238213

thanks Jamie

[jh2663]

I had very similar kind of errors as shown here. My solutions were to:

1. give a try reinstallation of 'NMF' package with ref='devel' option:

devtools::install_github("renozao/NMF",ref = 'devel', force=TRUE)

2. use different NMF algorithms such as 'lee' or 'nsNMF' instead of 'brunet'

My case had very few data points so 'brunet' algorithm failed to calculate the matrix properly for some reasons. Other algorithms work fine even for very sparse input matrix. FYI, I find 'nsNMF' looked more reasonable to my case.

Hope this helps,

[Sames-Jtudd]

cheers ill give that a go.

[Sames-Jtudd]

So that didn't work sadly.

[FunGeST]

Hi Jamie,

Thanks for getting in touch, and I'm sorry for not getting back to you sooner.

I haven't seen this issue before, even when working with sparse datasets as @jh2663 suggested. I notice you're using the older version of Palimpsest, would you be able to update your version of the package and let us know if you're still having the same problem? Hopefully that should fix it or at least make it easier for us to help you!

The latest version can be installed like this:

install.packages("devtools") library(devtools) devtools::install_github("FunGeST/Palimpsest", force = TRUE)

best wishes, Benedict

[Sames-Jtudd]

Hi Benedict,

Thanks for getting back to me, thought I had the most recent version, I’ll try that and fingers crossed it will work.

Best Jamie

From: FunGeST [email protected] Sent: 13 January 2020 11:53 To: FunGeST/Palimpsest [email protected] Cc: James Studd [email protected]; Author [email protected] Subject: Re: [FunGeST/Palimpsest] error using deconvolution_nmf (#34)

Hi Jamie,

Thanks for getting in touch, and I'm sorry for not getting back to you sooner.

I haven't seen this issue before, even when working with sparse datasets as @jh2663https://github.com/jh2663 suggested. I notice you're using the older version of Palimpsest, would you be able to update your version of the package and let us know if you're still having the same problem? Hopefully that should fix it or at least make it easier for us to help you!

The latest version can be installed like this: install.packages("devtools") library(devtools) devtools::install_github("FunGeST/Palimpsest", force = TRUE)

best wishes, Benedict

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[FunGeST]

Thanks! Please note that some of the function names have now changed, see the example script for more information on this (e.g. NMF_Extraction() has replaced deconvolution_nmf()).