Calculate the posterior fold change for each transcript across conditions

Description

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

Usage

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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

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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)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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