sigclust() not working

[melodyng]

Hi there. The sigclust function doesnt seem to be working. The reply "only one sample left" keeps appearing.
I hope you can help. Thanks

set.seed(1)
pam_4 <- ccomb_class2$4[, "PAM_Euclidean"]
sig_obj <- sigclust(hgsc, k = 4, nsim = 100, labflag = 0, label = pam_4)

[1] "Only one sample left, no need for clustering!"
num 0

[jlhanson5]

I ran into similar errors. I ran this basic code (from https://alinetalhouk.github.io/diceR/reference/sigclust.html):

data(hgsc)
dat <- hgsc[1:100, 1:50]
nk <- 4
cc <- consensus_cluster(dat, nk = nk, reps = 5, algorithms = "pam",progress = FALSE)
cl.mat <- consensus_combine(cc, element = "class")
lab <- cl.mat$4[, 1]
set.seed(1)
str(sigclust(x = dat, k = nk, nsim = 50, labflag = 1, label = lab))
[1] "Only one sample left, no need for clustering!"
num 0

here's my R sessionInfo--
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] RColorBrewer_1.1-2 Biobase_2.54.0 BiocGenerics_0.40.0 pander_0.6.5 ggplot2_3.3.5 dplyr_1.0.8
[7] diceR_1.1.0.9000

loaded via a namespace (and not attached):
[1] progress_1.2.2 gtools_3.9.2 tidyselect_1.1.2 clusterCrit_1.2.8 purrr_0.3.4 reshape2_1.4.4
[7] colorspace_2.0-3 vctrs_0.3.8 generics_0.1.2 NMF_0.23.0 utf8_1.2.2 rlang_1.0.2
[13] pillar_1.7.0 glue_1.6.2 withr_2.5.0 DBI_1.1.2 registry_0.5-1 rngtools_1.5.2
[19] foreach_1.5.2 lifecycle_1.0.1 plyr_1.8.6 stringr_1.4.0 pkgmaker_0.32.2 munsell_0.5.0
[25] gtable_0.3.0 codetools_0.2-18 labeling_0.4.2 doParallel_1.0.17 parallel_4.1.0 class_7.3-20
[31] fansi_1.0.2 Rcpp_1.0.8.3 xtable_1.8-4 scales_1.1.1 abind_1.4-5 farver_2.1.0
[37] hms_1.1.1 digest_0.6.29 stringi_1.7.6 grid_4.1.0 clue_0.3-60 cli_3.2.0
[43] tools_4.1.0 magrittr_2.0.2 clValid_0.7 tibble_3.1.6 cluster_2.1.2 RankAggreg_0.6.6
[49] tidyr_1.2.0 crayon_1.5.0 pkgconfig_2.0.3 ellipsis_0.3.2 gridBase_0.4-7 prettyunits_1.1.1
[55] assertthat_0.2.1 rstudioapi_0.13 iterators_1.0.14 R6_2.5.1 mclust_5.4.9 compiler_4.1.0'