I am using Aldex2 Version: 1.17.0 (Date: 2019-2-28) and I am having some issues following the tutorial I found here:
https://bioconductor.org/packages/devel/bioc/vignettes/ALDEx2/inst/doc/ALDEx2_vignette.pdf (check page 7 for complex study design and glm)
This is my command line:
covariates <- data.frame("A" = sample(0:1, 14, replace = TRUE), "B" = c(rep(0, 7), rep(1, 7))) mm <- model.matrix(~ A + B, covariates) selex.sub<- selex[1:400,] Xtestclr <- aldex.clr(selex.sub, mm, mc.samples=8, denom="all") glmTest <- aldex.glm(Xtestclr, mm) # #Features that are differential under any of the variables #should be validated using aldex.effect: XtestEffect<- aldex.effect(clr = Xtestclr)
I am receiving the following error:
#Error in aldex.effect(clr = Xtestclr) : # mismatch btw 'length(conditions)' and 'ncol(reads)'
I guess the problem is the clr output, which I should probably re-create it for individual variables ? I am not sure about it though., I would appreciate some advice on how to proceed.
Thank you for your kind attention, Max