Description Usage Arguments Value
Filtering of spot values by the condition PM > MM and spot intensity > spike in spot intensity
1 2 3 |
MA |
MAList object as defined by limma |
normMethod |
Optional normalization method name that attached to the log file name (e.g. _vsn_) |
subsetByManualControl |
Boolean, data may be subsetted by the spike in controls |
subsetByPMvsMMBoolean, |
data may be subsetted by restriction PM > MM |
ndups |
Number of duplicated spots |
spacing |
Placement of the duplicated spots (in default mode it is assumed that spots are sorted) |
weights |
Parameter for avedups function |
design |
Design of the experiment is considered when caluclating restrictions (subsetByManualControl,subsetByPMvsMM) |
writeLog |
Writes a log file of the filtering steps |
Filtered MA object
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