Generate statistics associated with pairwise differential expression
Description
When provided with an ExpressionSet
,
comparisons are made between control and perturbation samples.
Usage
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pairwise_compare(
eset,
control_perturb_col = "cmap",
control="control",
perturb="perturbation")
pairwise_compare_limma(
eset,
control_perturb_col = "cmap",
control="control",
perturb="perturbation",
limma.index=2)

Arguments
eset 

control_perturb_col 
Column name in 
control 
String designating control samples in the

perturb 
String designating perturbation samples in the

limma.index 
Integer specifying the index of the parameter estimate for which we to extract t and other statistics. The default corresponds to a twoclass comparison with the standard parameterization. The function assumes that there was no missing data, so that test for all genes were performed on the same sample size. 
Value
The function returns a data frame with the following columns:
log_fc 
Log foldchange between perturbed and control data. (A positive value denotes higher expression in the perturbed samples.) 
z 
When at least one condition has two or more samples, the
pairwise_compare_limma functions uses 
p 
When at least one condition has two or more samples, the
twotailed standard (pairwise_compare) or limma pvalue
(pairwise_compare_limma), as computed by 
Note
The pairwise_compare functions returns pvalues from a standard ttest. The pairwise_compare_limma functions uses the limma package instead to perform a moderated ttest.