MCMC.qpcr-package: Bayesian analysis of qRT-PCR data
In MCMC.qpcr: Bayesian Analysis of qRT-PCR Data

Description Details Author(s) References Examples

This package implements generalized linear mixed model analysis of qRT-PCR data so that the increase of variance towards higher Ct values is properly dealt with, and the lack of amplification is informative (function mcmc.qpcr). Sample-loading effects, gene-specific variances, and responses of all genes to each factor combination are all jointly estimated within a single model. The control genes can be specified as priors, with adjustable degree of expected stability. The analysis also works well without any control gene specifications.

For higher-abundance datasets, a lognormal model is implemented that does not require Cq to counts conversion (function mcmc.qpcr.lognormal).

For higher-abundance datasets datasets in which the quality and/or quantity of RNA samples varies systematically (rather than randomly) across conditions, the analysis based on multigene normalization is implemented (function mcmc.qpcr.classic).

The package includes several functions for plotting the results and calculating statistical significance (HPDplot, HPDplotBygene, HPDplotBygeneBygroup).

The detailed step-by-step tutorial is here: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/mcmc.qpcr.tutorial.pdf.

Package: MCMC.qpcr

Type: Package

Version: 1.2.3

Date: 2016-11-07

License: GPL-3

Mikhail V. Matz, University of Texas at Austin <matz@utexas.edu>

Matz MV, Wright RM, Scott JG (2013) No Control Genes Required: Bayesian Analysis of qRT-PCR Data. PLoS ONE 8(8): e71448. doi:10.1371/journal.pone.0071448

data(beckham.data)
data(beckham.eff)

# analysing the first 5 genes 
# (to try it with all 10 genes, change the line below to gcol=4:13)
gcol=4:8 
ccol=1:3 # columns containing experimental conditions

# recalculating into molecule counts, reformatting
qs=cq2counts(data=beckham.data,genecols=gcol,
condcols=ccol,effic=beckham.eff,Cq1=37)

# creating a single factor, 'treatment.time', out of 'tr' and 'time'
qs$treatment.time=as.factor(paste(qs$tr,qs$time,sep="."))

# fitting a naive model
naive=mcmc.qpcr(
	fixed="treatment.time",
	data=qs,
	nitt=3000,burnin=2000 # remove this line in actual analysis!
)

#summary plot of inferred abundances
#s1=HPDsummary(model=naive,data=qs)

#summary plot of fold-changes relative to the global control
s0=HPDsummary(model=naive,data=qs,relative=TRUE)

#correcting p-values for multiple comparisons
s0.adj=padj.hpdsummary(s0,controls=c("gapdh"))

# pairwise differences and their significances for each gene:
s0.adj$geneWise