function runMDS() do not work

[jlatreil]

Dear all,

than-you for your very nice package.

Describe the bug I ran the code below from the book "Orchestrating Microbiome Analysis with Bioconductor" in R and it does not work. Everything is ok until runMDS intruction. Any idea ? I put the version of R and of the packages that i used.

all the best

Julie

To Reproduce

library(mia) library(miaTime) library(miaViz) library(scater)

Example data

data("GlobalPatterns", package = "mia")

Data matrix (features x samples)

tse <- GlobalPatterns

some beta diversity metrics are usually applied to relative abundances

tse <- transformAssay(tse, method = "relabundance")

Add group information Feces yes/no

tse$Group <- tse$SampleType == "Feces"

Expected behavior -> but it do not work

Error in assay(x, exprs_values) : 'assay(, i="character", ...)' invalid subscript 'i' 'logcounts' not in names(assays())

Additional context

R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.6 (Ootpa)

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so

miaViz_1.6.0 miaTime_0.1.21
mia_1.9.16

[ake123]

Hi, I tested the functions and everything is working correctly in my end. I would recommend you to Update your R version (https://www.r-project.org/).

[antagomir]

Also miaViz current version is 1.9.1 (devtools::install_github("microbiome/miaViz") but that shouldnt affect this.

Does the error message occur in the transformAssay function call, or where exactly?

[antagomir]

The exprs_values is nowadays named assay.type, you can check assayNames(tse) and you need to specify one of these assays via assay.type argument.

[jlatreil]

it is this part which did not work. i will test with an update version of R

Perform PCoA

tse <- runMDS(tse, FUN = vegan::vegdist, method = "bray", name = "PCoA_BC", assay.type = "relabundance")

[antagomir]

Yes, update and let's see. Looking fwd!

[ake123]

@jlatreil did you manage to update to the latest version of R & the packages and test it?

[jlatreil73]

Hello, i tried and it's working now.

thank a lot