AD_data: Anaerobic digestion study
In EvaYiwenWang/PLSDAbatch: PLSDA-batch

AD_data

R Documentation

Anaerobic digestion study

Description

This study explored the microbial indicators that could improve the efficacy of anaerobic digestion (AD) bioprocess and prevent its failure. The samples were treated with two different ranges of phenol concentration (effect of interest) and processed at five different dates (batch effect). This study includes a clear and strong batch effect with an approx. balanced batch x treatment design.

Usage

data('AD_data')

Format

A list containing three TreeSummarizedExperiment objects FullData, EgData and CorrectData:

FullData: A TreeSummarizedExperiment object containing the counts of 75 samples and 567 OTUs. The meta data information of each sample is stored in the rowData, while the taxonomy of each OTU is stored in the colData.
EgData: A TreeSummarizedExperiment object containing the values of 75 samples and 231 OTUs filtered and centered log ratio transformed from the FullData with raw counts.The rowData includes Y.trt and Y.bat. Y.trt is the effect of interest, which is a factor of phenol concentrations for each sample in the AD study; Y.bat is the batch effect, which is a factor of sample processing dates for each sample. The taxonomy of each OTU is stored in the colData. The rowTree is built based on the Y.bat.
CorrectData: A TreeSummarizedExperiment object containing seven datasets before or after batch effect correction using different methods. Each assay includes 75 samples and 231 OTUs.

Value

None.

Source

The raw data were provided by Dr. Olivier Chapleur and published at the referenced article. Filtering and normalisation described in our package vignette.