sponge_data: Sponge _A. aerophoba_ study
In EvaYiwenWang/PLSDAbatch: PLSDA-batch

sponge_data

R Documentation

Sponge A. aerophoba study

Description

This study investigated the relationship between metabolite concentration and microbial abundance of specific sponge tissues. The samples were collected from two types of tissues (Ectosome vs. Choanosome) and processed on two separate denaturing gradient gels in electrophoresis. This study includes relative abundance data only and a completely balanced batch x treatment design.

Usage

data('sponge_data')

Format

A TreeSummarizedExperiment object containing the relative abundance (Tss_value) and centered log ratio transformed values (Clr_value) of 32 samples and 24 OTUs. The rowData includes Y.trt and Y.bat. Y.trt is the effect of interest, which is a factor of sponge tissues for each sample in the sponge study; Y.bat is the batch effect, which is a factor of electrophoresis gels where each sample processed. The rowTree is built based on the Y.bat.

Value

None.

Source

The raw data were downloaded from the referenced article. Filtering and normalisation described in https://evayiwenwang.github.io/PLSDAbatch_workflow/.