Comments (5)
Hi Peng,
The error is something internal in the aldex
function, and I cannot reproduce it. You can try the following: sample_data(TS)$Genotype <- as.character(sample_data(TS)$Genotype)
and then run it again. If this doesn't help, I need a reproducible example to figure out the problem.
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Hi Peng,
Regarding ALDEx2, it might be because I adjust p-values externally, but if you run through the CoDa workshop the ALDEx2 functions give you the adjusted p-values. Everything else just comes from the aldex
function. It's` hard to say what's correct. I'll look more into this.
Regarding DESeq2, I'm just running the data through the DESeq
function. Again, I adjust p-values externally, but with the same method as used in DESeq2 by default, so it should be the same. Are the raw p-values also different between the QIIME and the DAtest implementation?
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from datest.
Hi Peng
I think I have found out why you get different results.
Regarding ALDEx2, I have changed the code in the new version such that the p-value adjustment is now the one that ALDEx2 outputs. The other values (for example raw p-values) might appear different, but it is because of ALDEx2s Monte Carlo sampling which changes the output slightly every time you run it. If you want reproducible results run set.seed
before running ALDEx2.
Regarding DESeq2, it is probably because I use manual geometric means in my implementation, as suggested by these posts: joey711/phyloseq#387. In the new version of DAtest I also included the original DESeq2 (DA.ds2x). You can compare with this one, but beware, it appears to have higher false positive rates, at least for my test dataset.
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Related Issues (20)
- min.sample argument in preDA function HOT 1
- Errors in Mac Installation HOT 2
- Adding interaction terms in DA.neb() HOT 4
- Parallelization does not work in R 4.0 + Rstudio HOT 4
- Clarification on terminology of "raw counts" vs. "absolute abundance" HOT 2
- Preform comparisons on rank (i.e. family) level instead of OTU HOT 2
- Add corncob
- Cannot install HOT 2
- Phylum level - warning HOT 1
- Addition of ANCOM and ANCOM-BC HOT 4
- Error in rowSums HOT 6
- Implement UpsetDA
- Posthoc for aov with predictor and covar? HOT 1
- Getting error "subscript out of bounds" when trying to run testDA()
- Fail to install the DAtest HOT 2
- Best Practices for >2 treatments HOT 1
- DA.aov/DA.lao and DA.TukeyHSD HOT 4
- showing p-value on the graphs HOT 1
- Score = 0 for all tests and elaboration on running PCoA prior to DAtest HOT 1
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