Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

The Bimodality Index Selection (BI)

DK David Källberg
LV Linda Vidman
PR Patrik Rydén
request Request a Protocol
ask Ask a question
Favorite

For each gene, it is assumed that the density f(x) of the expression value can be described by a normal-mixture model with two components, i.e.,

where μA and μB denote the mean in the two subgroups and p is the proportion of samples in one group (Wang et al., 2009). The BI is defined as

The expectation-maximization (EM) algorithm was used to estimate the BI using the R package mixtools (Benaglia et al., 2009). Ten different starting values were used for the EM-algorithm, generated from a grid with 10 values for the fraction parameter p, evenly spaced between 0 and 1, for more details, see Karlis and Xekalaki (2003). Genes with high BI were selected for analysis.

Copyright and License information:  ©2021 Källberg, Vidman and Rydén.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A