p-value in CIBERSORT
1
0
Entering edit mode
7 weeks ago

Hello,

I'm doing some deconvolution analysis with CIBERSORT in R with the LM22 file but when I look at the results the p-value's column is all 9999. What I'm doing wrong?

results <- cibersort(LM22, at41)

enter image description here

CIBERSORT p-value • 399 views
ADD COMMENT
2
Entering edit mode
6 weeks ago
Aspire ▴ 340

You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutations is 0. It is not possible to calculate a p-value by permutations when no permutations are used. Hence I believe that the authors of the package deliberately used such a number which is clearly not a probability, to show that clearly.

Cibersort code

cibersort <- function(sig_matrix, mixture_file, perm = 0, QN = TRUE){
  ..
  P <- perm #number of permutations
  ..
  pval <- 9999
  ..
  if (P > 0) {
      pval <- 1 - (which.min(abs(nulldist - mix_r)) / length(nulldist))
  }
  ..
}

So, you can see from the code that if perm==0 (default), the pval is left with the value of 9999

ADD COMMENT
0
Entering edit mode

Thank you so much!!

ADD REPLY

Login before adding your answer.

Traffic: 2515 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6