CATPlots {applera}R Documentation

CATplots is a quality control function to evaluate replicates quality

Description

This function is used to evaluate the quality of biological replicates using the CAT plots originally develped by Irizarry in Nature Methods 2005. The function has been build for comparing replicate quality in a two groups experiment (e.g. test set vs reference set).

Usage

CATPlots(object, cond, minGenes=25, maxGenes=1000, upsideDown=FALSE)

Arguments

object An applera object, or an exprSet object or a matrix of expression values, where columns are arrays replicates and rows are genes.
cond A vector of 0 and 1, where 1 indicates the group of test arrays (Trt) to be evaluated with respect to a group of reference arrays (Ctrl) indicated by 0.
minGenes Min number of genes to be used to create the gene lists. For more information see the applera vignette.
maxGenes Max number of genes to be used to create the gene lists. For more information see the applera vignette.
upsideDown A logical parameter that allows to perfome CATplots also on the reversed condition vector, where 0s are now 1s and 1s are 0s.

Details

See applera vignette

Value

Results are represented as plots and the function returns a list.

resultR2Trt R-squared correlation among Trt data.
resultR2Crt R-squared correlation among Ctrl data.

Note

Author(s)

Francesca Cordero <fcordero@di.unito.it>

References

Examples

# data(test)
# tmp1 <- exprs(signal(test))
# tmp2 <- CATPlots(tmp1, c(0,0,0,1,1,1), 1, 1000, FALSE)

[Package applera version 1.4.0 Index]