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mcalgaro93 / benchdamic

Benchmark of differential abundance methods on microbiome data
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Update DA_ALDEx2 function #1

Closed sdgamboa closed 2 years ago

sdgamboa commented 2 years ago

Hello, @mcalgaro93. I'd like to report what I think is a bug in the DA_ALDEx2 function. The "wilcox" option of the test argument throws an error. Other options, which would be valid in the original ALDEx2::aldex function, throw an error as well. Please see the reprex below.

After checking the code of the function, I assumed that the DA_ALDEx2 function only supports Welch's t and Wilcoxon tests. With that in mind, I wrote a couple of simple fixes and updated the documentation.

I hope this information is helpful and thank you for considering these fixes.

suppressMessages({
    library(benchdamic)
})

data("ps_plaque_16S")
ps <- ps_plaque_16S
ps <- norm_edgeR(ps, 'none')
#> NF.none column has been added.

## t test works
output_t <- DA_ALDEx2(
    ps, conditions = "HMP_BODY_SUBSITE", test = 't', norm = 'none',
    verbose = FALSE
)

## 'wilcox' doesn't work
output_wilcox <- DA_ALDEx2(
    ps, conditions = "HMP_BODY_SUBSITE", test = 'wilcox', norm = 'none',
    verbose = FALSE
)
#> Error in ALDEx2::aldex(reads = norm_counts, conditions = conditions, mc.samples = mc.samples, : argument 'test' not recognized

## Other valid inputs for ALDEx2 don't work either
output_kw <- DA_ALDEx2(
    ps, conditions = "HMP_BODY_SUBSITE", test = 'kw', norm = 'none',
    verbose = FALSE
)
#> Error in DA_ALDEx2(ps, conditions = "HMP_BODY_SUBSITE", test = "kw", norm = "none", : Please choose between p-values produced by Welch t-test (t) or by the Wilcoxon test (wilcox).

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
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#>  date     2022-03-20
#>  pandoc   2.17.1.1 @ /usr/lib/rstudio/bin/quarto/bin/ (via rmarkdown)
#> 
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Created on 2022-03-20 by the reprex package (v2.0.1)

mcalgaro93 commented 2 years ago

Hello @sdgamboa. Yes, for now the function DA_ALDEx2 supports only t and wilcox tests. I forgot to mention it in the manual. Thank you for finding and fixing that bug.