Question: Aldex2 error following tutorial - complex study design
1
4 months ago by
mstagliamonte0 wrote:

Hi,

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

software error aldex2 • 89 views