Entering edit mode
Good morning,
I would like to ask for help when running PROPER. When I set the ngenes 600, the results table returns NaN. for higher countsof ~16k or more I get results just fine.
Are there any adjustments that i can make when using gene counts in the 100's?
Thank you,
Carl
# References to Bioconductor
# Manual https://www.bioconductor.org/packages/release/bioc/manuals/PROPER/man/PROPER.pdf
# Article & Samples https://www.bioconductor.org/packages/release/bioc/vignettes/PROPER/inst/doc/PROPER.pdf
#options(pkgType = "binary")
#if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#options(pkgType = "binary")
#BiocManager::install("PROPER")
library(PROPER)
## specify some parameters: generate baseline expression and
## dispersion from Bottom data, and specify a function for
## alternative log fold changes.
fun.lfc=function(x) rnorm(x, mean= 12, sd= 1.5)
# Key points
# Use the latest Bioconductor release version. Ensure that your packages are up-to-date.
# Post all of your R code.
# Include a copy of any error or warning messages that appeared in R.
# If your question involves experimental data, include an example of the sample-level covariate data (one row per sample, one column per covariate). If it would help answer your technical question, and can be shared, explain the motivation behind your experiment.
# Always paste the output of sessionInfo() at the end of your post.
# If possible, provide a minimal, self-contained example that someone else can cut-and-paste into a new R session to reproduce your problem.
#If the example produces an error, provide the output of traceback() after the error occurs.
# 16000
simOptions=RNAseq.SimOptions.2grp(ngenes= 600, seqDepth=2000000,lBaselineExpr= "cheung",
lOD="cheung", p.DE=0.05, lfc=fun.lfc)
summary(simOptions)
simRes = runSims(Nreps=c(2,3,4,5), sim.opts = simOptions, nsims=500,
DEmethod= "edgeR")
powers = comparePower(simRes)
power.seqDepth(simRes, powers)
#plotPower(powers)
plotAll(powers)
######## SS=2,2 SS=3,3 SS=4,4 SS=5,5
# 0.2 NaN NaN NaN NaN
# 0.5 NaN NaN NaN NaN
# 1 NaN NaN NaN NaN
# 2 NaN NaN NaN NaN
# 5 NaN NaN NaN NaN
# 10 NaN NaN NaN NaN
# sessionInfo()
# R version 4.0.2 (2020-06-22)
# Platform: x86_64-apple-darwin17.0 (64-bit)
# Running under: macOS 10.16
#
# Matrix products: default
# LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] edgeR_3.30.3 limma_3.44.3 PROPER_1.20.0
#
# loaded via a namespace (and not attached):
# [1] Rcpp_1.0.6 locfit_1.5-9.4 lattice_0.20-44 packrat_0.6.0 digest_0.6.27 grid_4.0.2 HDInterval_0.2.2
# [8] evaluate_0.14 rlang_0.4.11 rmarkdown_2.8 tools_4.0.2 xfun_0.22 yaml_2.2.1 compiler_4.0.2
# [15] BiocManager_1.30.15 htmltools_0.5.1.1 knitr_1.33 #