PostFC: Calculate the posterior fold change for each transcript...
In EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

Description Usage Arguments Value Author(s) References See Also Examples

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

1	PostFC(EBoutput, SmallNum = 0.01)

`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.

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.

Ning Leng

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)

EBTest, GetMultiFC

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)

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