Getting error "subscript out of bounds" when trying to run testDA()

[gbergmann]

Describe the bug Hello, a collaborator recommended I try the DAtest package for differential abundance analysis on some phyloseq data of mine. I'm still learning how to use the package, so the error is most likely due to a problem with how I've set up my data. When I try to run testDA() on one of my datasets, I get the error "Error in { : task 1 failed - "task 1 failed - "subscript out of bounds." This has happened both when I use the transposed OTU table and a vector of my sample group (i.e. plant tissue type) levels as the predictor, as well as when I use the source phyloseq object and the sample groups from my metadata. Any suggestions on how to resolve this problem are much appreciated!

To Reproduce Here's the code I tried, and the resulting error: (csv file is attached for reproducibility) seed.stigma.raw.asv.csv

seed.stigma.raw.asv <- otu_table(seed.stigma.raw.phy) %>% data.frame() seed.stigma.raw.asv.t <- t(seed.stigma.raw.asv) %>% data.frame() vec <- c("stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "stigma", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled", "seed_pooled") test <- testDA(seed.stigma.raw.asv.t, predictor = vec) test2 <- testDA(seed.stigma.raw.phy, predictor = "tissue_type") options(error=recover)

Seed is set to 123 predictor is assumed to be a categorical variable with 2 levels: seed_pooled, stigma |=================================================================================================| 100%neb, per, adx, vli, qpo, poi, wil, ttt, ltt, ltt2, ds2, ds2x, lim, lli, lli2, lrm, llm, llm2 were excluded due to failure Error in { : task 1 failed - "task 1 failed - "subscript out of bounds"" In addition: Warning messages: 1: In tests != c("lim", "lli", "lli2", "vli") : longer object length is not a multiple of shorter object length 2: In tests != c("lim", "lli", "lli2", "vli") : longer object length is not a multiple of shorter object length

OS and package versions (please complete the following information):

• OS: MacOS Ventura 13.3.1
• DAtest version: 2.7.5
• Versions of other packages related to the bug: DESeq2_1.40.2