Differential expression analysis based on the total counts difference.
This function performs a default analysis by calling, in order, the functions:
defualt is 'BH', method for p-value adjusted, see
default is TRUE, switch for outlier replacement.
default is FALSE, whether to print messages at each step
parameters passed to
The differential expression analysis models the total counts difference by a Negative binomal distribution
an ABSDataSet object with additional elements, which can be retrieved by
Amean and Bmean, mean of log2 normalized reads count for group A and B,
foldChange, shrinked (expression level and gene-specific) log2 of fold-change, B - A,
rawFC, raw log2 of fold-change, B-A (without shrinkage),
lowFC, expression level corrected log2 fold-change,
pvalue, pvalue from NB distribution model,
adj.pvalue, adjuested p-value used p.adjust method.
Wentao Yang, Philip Rosenstiel & Hinrich Schulenburg: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
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