ggloor / ALDEx_bioc

ALDEx_bioc is the working directory for updating bioconductor
27 stars 13 forks source link

`aldex.effect` returns the same effect for every feature when `CI=T` #45

Closed amorris28 closed 2 years ago

amorris28 commented 2 years ago

Not sure if this was intended, but when I run aldex.effect with CI=T true:

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):

          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.

> packageVersion("ALDEx2")
[1] ‘1.24.0’

Thanks!

ggloor commented 2 years ago

This is now fixed in version 1.26.0