excuse me ,I am facing an issue when running CIBERSORT package:
when I try this:
library(CIBERSORT)
sig_matrix <- system.file("extdata", "LM22.txt", package = "CIBERSORT")
mixture_file <- system.file("extdata", "exampleForLUAD.txt", package = "CIBERSORT")
data(LM22)
LM22[1:4,1:4]#547 22
# B cells naive B cells memory Plasma cells T cells CD8
#ABCB4 555.71345 10.74423 7.225819 4.31128
#ABCB9 15.60354 22.09479 653.392328 24.22372
#ACAP1 215.30595 321.62102 38.616872 1055.61338
#ACHE 15.11795 16.64885 22.123737 13.42829
data(mixed_expr)
mixed_expr[1:4,1:4]#[1] 20501 5
# TCGA-05-4244-01 TCGA-05-4249-01 TCGA-05-4250-01 TCGA-05-4382-01
#A1BG 26.0302 120.1349 50.8597 145.9037
#A1CF 0.0000 0.3220 0.0000 0.0000
#A2BP1 1.7454 1.6098 0.0000 0.0000
#A2LD1 135.5022 89.0629 151.1332 112.0685
and running it:
> results <- cibersort(sig_matrix = LM22, mixture_file = mixed_expr,perm = 1000,QN = T)
Error in normalize.quantiles(Y) :
ERROR; return code from pthread_create() is 22
how can I do for this error?
hoping your help ......
excuse me ,I am facing an issue when running CIBERSORT package:
when I try this:
and running it:
how can I do for this error?
hoping your help ......