summarizeIntensitiesAsMedian: Summarizes the probe intensity as median of replicates...

In MiChip: MiChip Parsing and Summarizing Functions

Description

As the probes are spotted onto the in quaduplet or duplicate the values have to be combined in some way. This function takes the median of the intensities for the spots. Effectively the mean for duplicates. If less than half of the spots are present an NA is added

Usage

	summarizeIntensitiesAsMedian(eset,minSumlength=0, madAdjust=FALSE)

Arguments

eset	ExpressionSet containing probe intensity data to be summarized
minSumlength	The lowest acceptable length of the matrix to calculate a median
madAdjust	if TRUE then summarized data will be filtered according to the MAD median absolute deviation and set to NA if the median is less than MAD

Examples

#Calculate the median of a matrix omiting NAs
## Not run: 
summarizeIntensitiesAsMedian(eset,minSumlength=0,madAdjust=TRUE)

## End(Not run)

MiChip documentation built on Nov. 8, 2020, 8:01 p.m.