About ComBat-Seq

Overview

ComBat-Seq is a batch effect adjustment tool for bulk RNA-seq count data. Improved model based on ComBat.

Parameters

To run ComBat Seq, these inputs are used:

1. input matrix (required)
   • The input matrix is a counts matrix with dimensions gene x sample. The input counts matrix. Can be a .GCT or a .tsv (tab separated value) file. Rows should be genes, column should be samples, and the value are counts. File format documentation for GCT files: https://www.genepattern.org/file-formats-guide Some sample inputs can be found here: https://github.com/genepattern/ComBat_Seq/tree/develop/data
   • The input matrix should have corresponding sample names for the first row, and corresponding genes for the first column.
     

Example input matrix:

Name	Sample 1 Name	Sample 2 Name	Sample 3 Name	Sample 4 Name	Sample 5 Name	...	Sample m Name
Gene 1 Name	30	49	554	394	345	...	33
Gene 2 Name	839	485	123	223	339	...	234
...	...	...	...	...	...	...	...
Gene n Name	423	442	123	553	754	...	22

2. batch information (required)
   • Batch information contain information on batches. It is a table that looks like the following:
   • The file can be a .CLS file contaning only batch information, or a .tsv (tab separated file) containing batch, group, and any other additional information as long as it follows the format below.
     

Example batch information file

Samples	Sample 1 Name	Sample 2 Name	Sample 3 Name	Sample 4 Name	Sample 5 Name	...	Sample m Name
Batch	1	1	2	2	2	...	4
Group	Group 1 info	Group 1 info	Group 1 info	Group 1 info	Group 1 info	...	Group 3 info
...	...	...	...	...	...	...	...

3. covariates (optional)
   • Row names for covariates to use for this run of ComBat Seq.
4. output prefix (required)
   • Prefix for output filenames.

Advanced Parameters

5. Shrink
   • Whether to apply empirical Bayes estimation on dispersion.
6. gene subset n
   • Number of genes to use in empirical Bayes estimation, only useful when shrink = Yes
7. covariance matrix
   • If you wish to specify multiple biological variables. Model matrix for other covariates to include in the linear model besides batch and condition of interest.

Documentation

• ComBat-Seq author: Yuqing Zhang. Original GitHub Repo: https://github.com/zhangyuqing/ComBat-seq
• Docker image used: genepattern/combat_seq:v1

Citation

Yuqing Zhang, Giovanni Parmigiani, W Evan Johnson, ComBat-seq: batch effect adjustment for RNA-seq count data, NAR Genomics and Bioinformatics, Volume 2, Issue 3, 1 September 2020, lqaa078, https://doi.org/10.1093/nargab/lqaa078

Contact

• Edwin Huang: edh021@cloud.ucsd.edu