BLISS

Batch anaLysIS Suite (BLISS)

Project Description

The Batch anaLysIS Suite (BLISS) is intended to help identify batch effects in RNA expression data.  It has been tested on miRNA and mRNA results derived from the illumina sequencing platform.

There are 2 modes:

1. In a matched experiment (the same set of samples are sequenced twice) we can evaluate the significance of any systematic differences between the two runs.   This is meant to allow researchers to identify whether a change in technology is likely to introduce a batch effect.   We have used this to evaluate the differences between illumina sequencing pipelines.
2. A De Novo mode can take a matrix of expressions and subdivide the samples into the most prominent groups.   These results can then be used by a researcher to check for batch effects by correlating the identified groups with any known external variables such as disease type, sex, or sequencing platform.

NOTE: This code is meant to promote community collaboration in technology evaluation,  all discussion is encouraged.