average {maDB}R Documentation

Average signal channels of a microarray experiment

Description

average allows to average replicated signal channels (or replicated features within a signal channel) of a MadbSet object.

Usage

average(object,average.which,log.scale=TRUE,method,array.names=NULL,v=TRUE,average.genes=TRUE,exclude.flagged=TRUE,only.good.spots=FALSE,...)

Arguments

object The MadbSet that contains the signal channels that should be averaged.
average.which A numerical vector defining which columns of the exprs (which signal channels) slot of the object should be averaged. e.g. if the exprs slot contains 4 column and the columns 1 and 3 respectiveley 2 and 4 contain the expression values of replicated samples, c(1,2,1,2) has to be submitted to average the replicated samples.
log.scale If the expression values should be log2 transformed before averaging.
method The averaging method (one of c("mean","median","tukey.biweight")).
array.names The names for the averaged signal channels (the colnames of the exprs slot in the returned EexprSet object).
v Display some verbose messages during the execution of the function.
average.genes If replicated spots / genes per signal channel should also be averaged (must have the same ID!).
exclude.flagged If features with a weight of 0 (in the weights slot, means feature was flagged bad by the scanning software) should not be used to calculate the average across replicates. Could be problematic when doing a dye swap normalization with only two arrays with this function and some features are flagged bad on one and not flagged bad on the other array (function will use only the value from the not flagged feature in this case). In this case it could be better submitting exclude.flagged=FALSE.
only.good.spots If only those features should be averaged across replicated arrays, that are not flagged bad in all arrays (Only for averaging accross arrays, not averaging within arrays!).
... Additional parameters for a optional filter function.

Details

This function allows to average measured intensities of replicated microarrays (technical replicates). If the weights slot of the MadbSet object is not NULL and the exclude.flagged parameter is set TRUE, all genes that have weight of 0 (e.g. were flagged as bad spots by the scanning software) are excluded from the calculation of the average expression values (see description of the attribute exclude.flagged for more information).

Value

A MadbSet object that contains the averaged expression values for replicated microarrays.

Author(s)

Johannes Rainer

References

See Also

MadbSet-class


[Package maDB version 1.10.0 Index]