[estimateSignatures] error

[Hchang77]

Hello

I run the example codes for maftools. ( TCGA LAML MAF file)

I have error message when I try estimageSignatures.

I can get successful results when I try other analysis with NMF package.

Regards,

############

laml.sign = maftools::estimateSignatures(mat = laml.tnm, nTry = 6)
-Running NMF for 6 ranks
Compute NMF rank= 2 ... Timing stopped at: 1.21 0.02 2.98
ERROR
Compute NMF rank= 3 ... Timing stopped at: 1.41 0 3.36
ERROR
Compute NMF rank= 4 ... Timing stopped at: 1.3 0 3.22
ERROR
Compute NMF rank= 5 ... Timing stopped at: 1.48 0.02 4.48
ERROR
Compute NMF rank= 6 ... Timing stopped at: 2.11 0.03 4.8
ERROR
Error in (function (...) : All the runs produced an error:
-#1 [r=2] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: non-conformable arrays
  -VCF to MAF conversion? #2 [r=3] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: non-conformable arrays
  -feature request: rainfall plot #3 [r=4] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: non-conformable arrays
  -Dockerizeit #4 [r=5] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: non-conformable arrays
  -CNV/RNAseq data into oncoplot #5 [r=6] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: non-conformable arrays

[ShixiangWang]

please load NMF package firstly.

[Hchang77]

Thank you for your rapid response.
I re-installed the NMF package and re-try the estimageSignatures according to your response.
However, I got the error again.
Can I ask you another solution for this?

[ShixiangWang]

@Hchang77 I see you used the example data. Could you show all commands, your R session and their output here?

like

library(maftools)
library(NMF)
...
sessionInfo()

[PoisonAlien]

Maybe use the pConstant = 0.1 and see if it helps.

[ShixiangWang]

@Hchang77 Yes, try @PoisonAlien suggested, the example data should add a small constant for avoiding the problem from NMF decomposition. I think pConstant = 1e-9 is okay.

[Hchang77]

Thank you for the nice anwer. The problem was solved.
And Thank you to the researchers who made this wonderful program.