ratio: Expression of the gene diazepam binding inhibitor (DBI)

In daniel-gerhard/qpcrmix: Mixed model analysis of qPCR data

Description

Two-way ANOVA in Randomized complete block design. Quantitative RT-PCR was used to study expression of the gene diazepam binding inhibitor (DBI) in the brain of piglets subject to weaning and social isolation treatments. The experimental layout followed a randomized complete block design (n = 3 litters) and the treatments consisted of a 2 x 2 factorial combination of weaning (early-weaned or non-weaned) and social isolation (isolated or control). Preliminary assays indicated that Sus scrofa 18S ribosomal RNA (18S) was suitable for use as an endogenous control gene and that the amplification efficiency for primers of the two genes (18S and DBI) was close to 2. All reactions were performed in triplicate but some observations were excluded from the analysis because of evidence of non-specific amplifications (as revealed by dissociation curve analyses).

Usage

data(ratio)

Format

A data frame with 134 observations on the following 8 variables.

Well

a factor

Sample

a factor

gene

factor with gene IDs: DBI or 18S as a control.

y

efficiency adjusted Ct levels

TRT

treatment factor (combination of weaning (early-weaned or non-weaned) and social isolation (isolated or control))

litter

the experimental unit (blocks)

wean

weaning treatment

iso

isolation treatment

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.

Examples

data(ratio)
qratio <- qpcr(data=ratio, response="y",
               gene="gene", control_gene="18S",
               fixed1="TRT", fixed2=NULL,
               rep_id="litter", block=TRUE,
               splitplot=FALSE,
               contrasts=TRUE, interaction=FALSE, adjusted=FALSE)

# model
qratio$model
# testing deltaCt contrasts
qratio$pvalues 

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