maanova (version 1.42.0)

dyeswapfilter: Gene filter for dye-swap experiment

Description

This function is used to flag the questionable spot in any kind of dye-swap experiment.

This function only works for 2-dye arrays.

Usage

dyeswapfilter(dataobj, r=4)

Arguments

dataobj

An object of class madata.

r

A cut-off value for bad spot. The genes with log-ratio difference larger than r times standard deviation will be flagged.

Value

An object of class rawdata or madata with the flag field created or updated.

Details

For each pair of dye-swap, the difference in log ratios (d) are computed. Then compute the IQR (interquartile range) of d and convert that to Standard Deviation by SD = IQR/1.35. Any gene with d larger than r times SD will be flagged.

Note that I assume in the input data object, the adjacent arrays is a dye-swap pair.

Examples

## Not run: 
# data(kidney)
# # riplot before filtering
# riplot(kidney.raw, array=1)
# # filter the gene
# rawdata <- dyeswapfilter(kidney.raw)
# # riplot again - some genes are highlighted
# riplot(rawdata, array=1)## End(Not run)