dyeswapfilter {maanova} | R Documentation |
This function is used to flag the questionable spot in any kind of dye-swap experiment.
This function only works for 2-dye arrays.
dyeswapfilter(dataobj, r=4)
dataobj |
An object of class |
r |
A cut-off value for bad spot. The genes with log-ratio difference larger than r times standard deviation will be flagged. |
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.
An object of class rawdata
or madata
with the
flag
field created or updated.
Hao Wu
## 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)