Error in cutree(h, k = nbasis(object))

[Sonia-Bedi]

Hi,

I am running the sig_estimate() with the following parameters and I have getting an error. What can I do to resolve this?

SE<-sig_estimate(NMF_matrix,range= 2:6, nrun = 10,use_random = FALSE,
method = "brunet",
seed = 123456,
cores = 1,
keep_nmfObj = FALSE,
save_plots = FALSE,
plot_basename = file.path(tempdir(), "nmf"),
what = "all",verbose = TRUE)

The error that I see is:

Error in cutree(h, k = nbasis(object)) :
elements of 'k' must be between 1 and 3
In addition: Warning message:
In (function (...) : NAs were produced due to errors in some of the runs:
-#3[r=4] -> elements of 'k' must be between 1 and 3 [in call to 'cutree']
-#4[r=5] -> elements of 'k' must be between 1 and 3 [in call to 'cutree']
-#5[r=6] -> elements of 'k' must be between 1 and 3 [in call to 'cutree']

[ShixiangWang]

Hi @Sonia-Bedi, could you print more message of your input matrix? like print(str(NMF_matrix)).

[Sonia-Bedi]

Surely

NMF_matrix = sig_tally_output$nmf_matrix

After print(str(NMF_matrix)), I got the following:

int [1:3, 1:96] 0 0 0 0 0 0 1 1 0 0 ...

• attr(*, "dimnames")=List of 2
  ..$ : chr [1:3] "test1" "test2" "test3"
  ..$ : chr [1:96] "A[T>C]A" "C[T>C]A" "G[T>C]A" "T[T>C]A" ...
  NULL

[ShixiangWang]

@Sonia-Bedi You only have 3 samples, it is not recommended to run sig_estimate(). If you really want to use it, you should set range= 2:6 as range = 2:3.

sig_fit is more recommended to quantify the signature activities.

[Sonia-Bedi]

Oh. Thank you for clearing it out. I am just learning all about it.

May I ask what is the minimum number of samples for which sig_estimate() is recommended?

[ShixiangWang]

My opinion is 10 at least. For sample size <30, I always recommend the signature fitting with sig_fit instead of de novo signature extraction with sig_estimate/extract.