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ggloor / ALDEx2_dev

ALDEx tool to examine compositional high-throughput sequence data with Welch's t-test
GNU Affero General Public License v3.0
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Can't use aldex.effect() on aldex.kw() object #28

Closed Rob-murphys closed 2 years ago

Rob-murphys commented 2 years ago

We can't use aldex.effect() on aldex.kw() object so how are we meant to understand the effect and plot it with the package?

x = aldex.clr(profile_nitrogen, conds = metadata$Timepoint, mc.samples = 32, denom = "all", verbose = F)

x.kw = aldex.kw(x)

x.effect = aldex.effect(x, CI=T, verbose=FALSE)

>Error in aldex.effect(x, CI = T, verbose = FALSE) : 
  only two condition levels are currently supported
mirpie commented 2 years ago

Hi, I believe currently aldex2 only supports two factor levels in your conditions vector, so if you have 3 timepoints it will throw an error. In order to handle a more complex design check out the docs for the aldex2.glm function

ggloor commented 2 years ago

you would need to calculate the effect for each condition pair manually if you use the glm function with more than two groups.