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.
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.
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)