workedExampleMedianNormalize {MiChip} | R Documentation |
Loads a set of hybridizations into a matrix and them proceeds to filter, summarize and median normalize them
workedExampleMedianNormalize(exptname, intensityCutoff=0, datadir=".", minSumlength, madAdjust = FALSE)
exptname |
string indicating the name of the experiment |
intensityCutoff |
The intensity value for accepting the spots intensity value in the experiment |
datadir |
The directory where hybridization files are found. |
minSumlength |
Minimum exceptable number of values to summarize intensity value. |
madAdjust |
if |
#Normalize data in the current directory to the median per chip datadir <- system.file("extdata", package="MiChip") myNormedEset <-workedExampleMedianNormalize("MyExpt", intensityCutoff=0, datadir, minSumlength=0, madAdjust=TRUE)