PostFC {EBSeq} | R Documentation

## Calculate the posterior fold change for each transcript across conditions

### Description

'PostFC' calculates the posterior fold change for each transcript across conditions.

### Usage

    PostFC(EBoutput, SmallNum = 0.01)

### Arguments

`EBoutput` | The ourput from function EBTest.
`SmallNum` | A small number will be added for each transcript in each condition to avoid Inf and NA. Default is 0.01.

### Value

Provide both FC and posterior FC across two conditions. FC is calculated as (MeanC1+SmallNum)/(MeanC2+SmallNum). And Posterior FC is calculated as:

# Post alpha P_a_C1 = alpha + r_C1 * n_C1

# Post beta P_b_C1 = beta + Mean_C1 * n_C1

# P_q_C1 = P_a_C1 / (P_a_C1 + P_b_C1)

# Post FC = ((1-P_q_C1)/P_q_c1) / ( (1-P_q_c2)/P_q_c2)

`PostFC` | The posterior FC across two conditions.
`RealFC` | The FC across two conditions (adjusted by the normalization factors).
`Direction` | The diretion of FC calculation.

### 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

EBTest, GetMultiFC

### Examples

    data(GeneMat)
    GeneMat.small = GeneMat[c(500:550),]
    Sizes = MedianNorm(GeneMat.small)
    EBOut = EBTest(Data = GeneMat.small,
    	Conditions = as.factor(rep(c("C1","C2"), each=5)),
    	sizeFactors = Sizes, maxround = 5)
    FC=PostFC(EBOut)

[Package EBSeq version 1.24.0 Index]