doPlotFCT {ABarray}R Documentation

Calculate fold change and t test, the plot

Description

Calculate fold changes and p values from t test, and plot the results using preset FDR threshold

Usage

doPlotFCT(eset, group, grpMember, order1 = NULL, order2 = NULL,
detectSample = 0.5, snThresh = 3, ...)

Arguments

eset eset eset an exprSet object
group which group from experiment design should calculation and plot be performed
grpMember optional group member within the group
order1 optional, For a pairwise comparison the ordering of the first group of replicates
order2 optional, For a pairwise comparison the ordering of the first group of replicates
detectSample
snThresh optional S/N ratio threshold. Default = 3
... Additional argument, currently not implemented

Details

Group members are optional. For example, if group name is "tissue", and group members in experiment design file include "brain", "liver", "lung", "muscle". We could include c("brain", "liver") as group member for the parameter, then t test will be performed between "brain" and "liver", and "lung" "muscle" will be ignored. However, if we omit group member in the arguments, all tissue members will be used for t test. In this case, there will be 6 pairwise t test between each member of the group.

If order1 and order2 are specified then a paired sample t-test will be conducted between the groups, with the arrays in each group sorted according to the ordering specified. For example, if order1 is c(1,3,2) and order2 is c(1,2,3), then the sample pairing is a1-b1, a3-b2, a2-b3, with a and b are subgroup 1 and subgroup 2 within the group.

The fold changes are difference between averaged subgroup1 expression vs averaged subgroup2. If paired t test is performed, the fold changes are calculated using each paired difference and take an average of paired difference.

Value

None. But a number of plot and result files will be produced.

Author(s)

Y Andrew Sun

Examples

#- doPlotFCT(eset, "sampleGroup", c("liver", "muscle"))
#- For a paired t test
#- doPlotFCT(eset, "sampleGroup", c("liver", "muscle"), order1 = c(1,2,3), order2 = c(1,3,2))

[Package ABarray version 1.4.2 Index]