error in DBS & ID denovo signatures extract

[shiguangyini]

Hello,

I got some errors using the above command. Hope you can any help.

DBS_denovo_sigs <- NMF_Extraction(input_matrices = DBS_input, range_of_sigs = 1:10, nrun = 10,
resdir = resdir)

Timing stopped at: 0.074 0 0.074 Timing stopped at: 35.24 11 9.273 geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? [1] The optimal number of DBS signatures is . [1] Extracting DBS signatures from the input samples.. Error: NMF::nmf - invalid argument 'rank': must be a single numeric value In addition: Warning messages: 1: In cor(d.consensus, d.coph, method = "pearson") : the standard deviation is zero 2: In (function (...) : NAs were produced due to errors in some of the runs: -#2[r=2] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run #1: non-conformable arrays -#3[r=3] -> NMF::nmf - 10/10 fit(s) threw an error.

I found someone had very similar kind of errors, but the solutions didn't work and I am using the newest version of the package.

#34 https://github.com/FunGeST/Palimpsest/issues/34

Is there any helpful solution for this? I look forward to hearing from you. Best wishes!

[benedict909]

Hi,

Thanks for reporting this, as you say it seems to be a common issue.

If you would be able to answer the following questions, hopefully I can try and work out what the cause is.

1. How many samples are in your input data?
2. Roughly how many mutations are there in each sample?
3. If you set the num_of_sigs argument to an integer (e.g. try 5) do you still receive this error?

Thank you for your help! Benedict