I have this " (1 stratum)" problem from vsn2 since 1/15/2021, even when I ran the sample codes (from https://www.bioconductor.org/packages/release/bioc/vignettes/vsn/inst/doc/A-vsn.R). I uninstalled and reinstalled my R several times, the problem has not been solved.
Please find the codes and output from R below.
Anyone has any idea on solving the problem?
Thanks for your help.
> library("vsn") Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > data("kidney") > xnorm = justvsn(kidney) vsn2: 8704 x 2 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > sessionInfo( ) version 4.0.3 (2020-10-10) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 10 x64 (build 18363) Matrix products: default locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods  base