qpcr: Mixed model analysis of qpcr data

Description Usage Arguments Value Author(s) References See Also

Description

Fits a linear mixed model to qpcr data, allowing for several genes, two-factorial block and split-plot designs. Delta-Ct and DeltaDelta-Ct values are calculated by multiple contrasts.

Usage

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qpcr(data, response, gene, control_gene, fixed1, fixed2 = NULL, rep_id,
block = FALSE, splitplot = FALSE, contrasts=TRUE, interaction=FALSE,
adjusted = FALSE, df=NULL)

Arguments

data

A data.frame object.

response

Name of a column in data, denoting a numeric response vector, usually estimated Ct values.

gene

Name of a column in data, denoting a factor coding for different genes.

control_gene

Name of a single control gene in the vector of gene names.

fixed1

Name of a column in data, denoting a factor coding for several treatment groups

fixed2

Name of a column in data, denoting a second factor coding for several treatment groups, default is NULL

rep_id

Name of a column in data, denoting a factor which identifies a biological replication or block.

block

Logical; are the rep_ids denoting a block variable? default is FALSE.

splitplot

Logical; Is the experiment designed as a split-plot with fixed1 as mainplots and fixed2 as subplot? default is FALSE.

contrasts

Logical; If TRUE: Tests for general linear hypotheses are performed.

interaction

Logical; If TRUE: Tests for interaction between fixed1 and fixed2 are performed if contrasts==TRUE.

adjusted

Logical; Should multiplicity adjusted p-values be reported? default is FALSE.

df

Providing degrees of freedom as a numeric value, an input of NULL corresponds to the assumption of a Normal- instead of a t-distribution.

Value

An object of class qpcrmacro.

Author(s)

Daniel Gerhard <gerhard@biostat.uni-hannover.de>

References

Steibel, JP, Poletto, R, Coussens, PM, Rosa, GJM (2009): A powerful and flexible linear mixed model framework for the analysis of relative quantification RT-PCR data. Genomics 94:146–152.

See Also

lmer, glht


daniel-gerhard/qpcrmix documentation built on May 14, 2019, 3:39 p.m.