Plot the Quality of Biological Replicates

This function performs several quality checks to validate the biological variation between replicates and stages (experiments).

Usage

PlotReplicateQuality(
  ExpressionSet,
  nrep,
  FUN = function(x) log(stats::var(x)),
  legend.pos = "topleft",
  stage.names = NULL,
  ...
)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

nrep

either a numeric value specifying the constant number of replicates per stage or a numeric vector specifying the variable number of replicates for each stage position.

FUN

a function that should be applied to quantify the variablity or quality of replicates. The default function is the log(var(x)) quantifying the variance between replicates.

legend.pos

the position of the legend, e.g. 'topleft', or 'topright' (see legend).

stage.names

a character vector specifying the stage names.

...

additional graphics parameters.

Details

The following quality checks can be performed:

• Quantification of variability between replicates as density function.

Author

Hajk-Georg Drost

Examples

data(PhyloExpressionSetExample)

# visualize log(var(x)) between replicates for each gene and developmental stage 
PlotReplicateQuality(ExpressionSet = PhyloExpressionSetExample[1:5000 , 1:8],
                     nrep          = 2,
                     legend.pos   = "topright",
                     ylim          = c(0,0.2),
                     lwd           = 6)