EBSeq (version 1.12.0)

GetMultiFC: Calculate the Fold Changes for Multiple Conditions

Description

'GetMultiFC' calculates the Fold Changes for each pair of conditions in a multiple condition study.

Usage

GetMultiFC(EBMultiOut, SmallNum = 0.01)

Arguments

EBMultiOut

The output of EBMultiTest function.

SmallNum

A small number will be added for each transcript in each condition to avoid Inf and NA. Default is 0.01.

Value

FCMat

The FC of each pair of comparison (adjusted by the normalization factors).

Log2FCMat

The log 2 FC of each pair of comparison (adjusted by the normalization factors).

PostFCMat

The posterior FC of each pair of comparison.

Log2PostFCMat

The log 2 posterior FC of each pair of comparison.

CondMean

The mean of each transcript within each condition (adjusted by the normalization factors).

ConditionOrder

The condition assignment for C1Mean, C2Mean, etc.

Details

Provide the FC (adjusted by the normalization factors) for each pair of comparisons. A small number will be added for each transcript in each condition to avoid Inf and NA. Default is set to be 0.01.

References

Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M.G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, and Christina Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013)

See Also

EBMultiTest, PostFC

Examples

data(MultiGeneMat)
MultiGeneMat.small = MultiGeneMat[201:210,]

Conditions = c("C1","C1","C2","C2","C3","C3")

PosParti = GetPatterns(Conditions)
Parti = PosParti[-3,]

MultiSize = MedianNorm(MultiGeneMat.small)

MultiOut = EBMultiTest(MultiGeneMat.small, 
	NgVector=NULL, Conditions=Conditions, 
	AllParti=Parti, sizeFactors=MultiSize, 
	maxround=5)

MultiFC = GetMultiFC(MultiOut)