dyeswapfilter {maanova} | R Documentation

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

### 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 adjecent arrays is a dye-swap pair.

### Value

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

### Author(s)

Hao Wu

### 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)

[Package maanova version 1.6.0 Index]