vegan:adonis with random effects?
Hi everyone,
Do you know if adonis from vegan package allows for random effects? If not, is there any function able to perform PERMANOVA with random effects?
Thanks in advance
16s
metagenomics
microbiome
• 2,095 views
•
link
written
by
andrebolerbarros
0
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Random effect model RNAseq
written by a.stef.44 1Hi everyone, I would like to perform random effect model (RMA) using LFC from DESeq2 and Var. I have four different studies and I planned …
-
How to use lme4() to perform differential expression on bulk RNA seq data with multiple random effe…
written by bioyas 2Hi everyone, I am dealing with bulk RNA-seq data that has one fixed effect (Condition) and two random effects (Patient info and batch info). I …
-
Multi Alignment - How to deal with uncertainty?
written by andrebolerbarros 0Hi everyone, I have samples which align with two different genomes with a great degree of similarity. Is there any way to handle/correct/take into consideration …
-
Doubt about adonis( ) on Beta diversity matrix
written by leandro 0Good evening, I have a little doubt about using function adonis( ) on R to apply a PERMANOVA on beta diversity matrix: it's done to …
-
post-hoc (Tukey) on adonis (permanova)
written by mario_de_manner 2Hello, I have a bray-curtis distance matrix and found significant associations on a grouping variable with adonis (permanova) using R package vegan. Now I would …
-
Normalize for sample size in 16S a-diversity analysis
written by bpvalderrama 3Hi everyone! I'm working with 6 samples of 16S microbiome data in R. When looking for correlation between sample size and diversity it seems to …
-
PERMANOVA on multiple groups if one or more differ in multivariate dispersion?
written by even.s.riiser 1Dear all, My previous microbiome statistical analysis has been based on normalized order-level metagenomic read counts of samples from two experiment groups. After confirming that …
-
How to do core genome accumulation curve using Vegan
written by Heraud 0Hi, I am doing a bacterial pangenomic analysis comparing different strains. I used Vegan package in R to plot the pangenome accumulation curve: library(vegan) specaccum(bin-matrix,"random",permutations=100) …
-
Removal of rare OTUs before calculating community distances / ADONIS / NMDS
written by dmcleanuk 3Hi, I have a large 16s microbiome dataset with some 600 samples spanning across 5 clinical groups which consists of around 6000 OTUs. I have …
-
Batch ID in TCGA database
written by Na Sed 31Hi, I have downloaded some data from TCGA and I need to remove their batch effects using 'combat' algorithm from sva package, but 'combat' function …
hi did you find a solution?