rtpcr (version 2.0.2)

qpcrMeans: Fold change (\(\Delta \Delta C_T\) method) analysis using a model

Description

Fold change (\(\Delta \Delta C_T\) method) analysis using a model object produced by the qpcrANOVAFC or qpcrREPEATED.

Usage

qpcrMeans(model, specs, p.adj = "none")

Value

Table of FC values, significance and confidence interval.

Arguments

model

an `lmer` fitted model object created by qpcrANOVAFC or qpcrREPEATED functions

specs

A character vector specifying the names of the predictors over which FC values are desired

p.adj

Method for adjusting p values

Author

Ghader Mirzaghaderi

Details

The qpcrMeans function performs fold change (\(\Delta \Delta C_T\) method) analysis using a model produced by the qpcrANOVAFC or qpcrREPEATED. The values can be returned for any effects in the model including simple effects, interactions and slicing if an ANOVA model is used, but ANCOVA models returned by rtpcr package only include simple effects.

Examples

# Returning fold change values from a fitted model.
# Firstly, result of `qpcrANOVAFC` or `qpcrREPEATED` is 
# acquired which includes a model object:
res <- qpcrANOVAFC(data_3factor, numberOfrefGenes = 1, mainFactor.column = 1, block = NULL)

# Returning fold change values of Type levels from a fitted model:
qpcrMeans(res$lm_ANOVA, specs = "Type")

# Returning fold change values of Conc levels from a fitted model:
qpcrMeans(res$lm_ANOVA, specs = "Conc")

# Returning fold change values of Conc levels sliced by Type:
qpcrMeans(res$lm_ANOVA, specs = "Conc | Type")

# Returning fold change values of Conc levels sliced by Type*SA:
qpcrMeans(res$lm_ANOVA, specs = "Conc | (Type*SA)")