amp.eff

Fold-amplification within each PCR cycle for each qRT-PCR assay. Determined by qPCR of
serial dilutions of the template (see Pfaffl 2001, Nucleic Acids Res 29:00)

datasets

Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: <https://matzlab.weebly.com/uploads/7/6/2/2/76229469/mcmc.qpcr.tutorial.v1.2.4.pdf>.

Mikhail Matz

MCMC.qpcr

Bayesian Analysis of qRT-PCR Data

amp.eff function

A data frame with 17 observations on the following 3 variables.<dl class="dl-horizontal">
 <dt><code>gene</code></dt><dd>a factor with levels <code>actin</code> <code>adk</code> <code>c3</code> <code>chrom</code> <code>clect</code> <code>eif3h</code> <code>g3pdh</code> <code>gsp2</code> <code>hsp16</code> <code>hsp60</code> <code>hsp90</code> <code>nd5</code> <code>r18s</code> <code>rpl11</code> <code>spon2</code> <code>tgoln</code> <code>ubl3</code></dd>
 <dt><code>efficiency</code></dt><dd>a numeric vector</dd>
 <dt><code>Cq1</code></dt><dd>a numeric vector</dd>
 </dl>

Format

amplification efficiencies and experimental Cq1 (optional column) — amp.eff

A data frame with 17 observations on the following 3 variables.<dl class='dl-horizontal'>
 <dt><code>gene</code></dt><dd>a factor with levels <code>actin</code> <code>adk</code> <code>c3</code> <code>chrom</code> <code>clect</code> <code>eif3h</code> <code>g3pdh</code> <code>gsp2</code> <code>hsp16</code> <code>hsp60</code> <code>hsp90</code> <code>nd5</code> <code>r18s</code> <code>rpl11</code> <code>spon2</code> <code>tgoln</code> <code>ubl3</code></dd>
 <dt><code>efficiency</code></dt><dd>a numeric vector</dd>
 <dt><code>Cq1</code></dt><dd>a numeric vector</dd>
 </dl>

amp.eff: amplification efficiencies and experimental Cq1 (optional column)

Description

Usage

Arguments

Format

Examples