example_data

<p>The first several rows of a dataset from the Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma
data collection, consisting of 5 genes from a dataset of raw RNA-Seq counts from 35 tumor and 35 normal samples.</p>

datasets

Implements the algorithm described in Jun Li and Alicia T. Lamere,
"DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes"  (Unpublished).
Detects not only genes that show different
average expressions ("differential expression", DE), but also genes that show different
diversities of expressions in different groups ("differentially dispersed", DD). DD genes
can be important clinical markers. 'DiPhiSeq' uses a redescending penalty on the
quasi-likelihood function, and thus has superior robustness against outliers and other noise.
Updates from version 0.1.0: (1) Added the option of using adaptive initial value for phi.
(2) Added a function for estimating the proportion of outliers in the data.
(3) Modified the input parameter names for clarity, and modified the output format for the main function.

Jun Li

DiPhiSeq

Robust Tests for Differential Dispersion and Differential
Expression in RNA-Sequencing Data

Alicia T. Lamere

example_data function

<p>A numeric matrix with five genes observed across 70 experiments. The first 35 are tumor samples,
  the second 35 are normal samples.</p>

example_data: Numeric count matrix of example data.

Description

Usage

Arguments

Format