GetMultiFC {EBSeq} | R Documentation

## 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.

### 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.

### 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.

### Author(s)

Ning Leng

### 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)

[Package EBSeq version 1.20.0 Index]