nakai


This is a log2-transformed two-group microarray (Affymetrix GeneChip) data
consisting of 31,099 probesets. A total of eight samples were taken from the
rat liver: the first four samples are fed and the last fours are 24-hour
fasted. The original data can be obtained from NCBI Gene Expression Omnibus
(GEO) with GSE7623. This is a subset.


datasets

This package provides a series of functions for performing
differential expression analysis from RNA-seq count data using
robust normalization strategy (called DEGES). The basic idea of
DEGES is that potential differentially expressed genes or
transcripts (DEGs) among compared samples should be removed
before data normalization to obtain a well-ranked gene list
where true DEGs are top-ranked and non-DEGs are bottom ranked.
This can be done by performing a multi-step normalization
strategy (called DEGES for DEG elimination strategy). A major
characteristic of TCC is to provide the robust normalization
methods for several kinds of count data (two-group with or
without replicates, multi-group/multi-factor, and so on) by
virtue of the use of combinations of functions in depended
packages.

Jianqiang Sun

TCC: Differential expression analysis for tag count data with
robust normalization strategies

nakai function

<code>nakai</code> is a matrix of 31,099 rows (probesets) and 8 columns
(samples or tissues).

Format

This is a log2-transformed two-group microarray (Affymetrix GeneChip) data
consisting of 31,099 probesets. A total of eight samples were taken from the
rat liver: the first four samples are fed and the last fours are 24-hour
fasted. The original data can be obtained from NCBI Gene Expression Omnibus
(GEO) with GSE7623. This is a subset.

nakai: DNA microarray data set

Description

Usage

Arguments

Format

References

Examples