Closed jlatreil closed 10 months ago
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/).
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?
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.
it is this part which did not work. i will test with an update version of R
tse <- runMDS(tse, FUN = vegan::vegdist, method = "bray", name = "PCoA_BC", assay.type = "relabundance")
Yes, update and let's see. Looking fwd!
@jlatreil did you manage to update to the latest version of R & the packages and test it?
Hello, i tried and it's working now.
thank a lot
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