Closed amorris28 closed 2 years ago
Not sure if this was intended, but when I run aldex.effect with CI=T true:
aldex.effect
CI=T
library(ALDEx2) data(selex) #subset only the last 400 features for efficiency selex.sub <- selex[1:400,] conds <- c(rep("NS", 7), rep("S", 7)) x <- aldex.clr(selex.sub, conds, mc.samples=16, denom="all", verbose=F) x.tt <- aldex.ttest(x, paired.test=FALSE, verbose=FALSE) x.effect <- aldex.effect(x, CI=T, verbose=FALSE)
I get the following warning message:
Warning message: In `[<-.data.frame`(`*tmp*`, , "effect", value = list(A.D.A.D = 0.389216468913272, : provided 400 variables to replace 1 variables
In addition, the effect size for every feature is the same: head(x.effect):
head(x.effect)
rab.all rab.win.NS rab.win.S diff.btw diff.win effect effect.low effect.high overlap A:D:A:D 1.6184457 1.5348357 2.4230976000 0.9501965 1.884682 0.3892165 -7.1442947 7.880041 0.303577600 A:D:A:E 1.8755323 1.7308237 4.1384033440 2.3785252 2.612724 0.3892165 -2.1461480 33.322191 0.178585980 A:E:A:D 4.0922976 1.6192446 10.8158345963 9.0471803 2.798459 0.3892165 0.9335586 47.982430 0.001251685 A:E:A:E 3.9880691 1.8622371 13.8362096327 11.8613215 2.610221 0.3892165 0.8246365 99.360670 0.001251685 A:D:C:D 0.5622123 0.6522687 -0.0987685742 -0.7302527 2.395500 0.3892165 -13.3358885 1.457304 0.375003543 A:D:C:E 0.5748159 0.6276297 0.0003990424 -0.5576256 2.680115 0.3892165 -11.0280915 1.751100 0.428573366
Is this intended? I'm maybe misunderstanding the CI flag, but I would like to somehow present a figure with effect sizes +/- the 95% CI for significant taxa.
CI
> packageVersion("ALDEx2") [1] ‘1.24.0’
Thanks!
This is now fixed in version 1.26.0
Not sure if this was intended, but when I run
aldex.effect
withCI=T
true:I get the following warning message:
In addition, the effect size for every feature is the same:
head(x.effect)
:Is this intended? I'm maybe misunderstanding the
CI
flag, but I would like to somehow present a figure with effect sizes +/- the 95% CI for significant taxa.Thanks!