Worked Example of MiChip Processing

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Description

Loads a set of hybridizations into a matrix and them proceeds to filter and summarize these data

Usage

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workedExampleNotNormalizedData(exptname, intensityCutoff=0, datadir=".", minSumlength, madAdjust = FALSE )

Arguments

exptname

string indicating the name of the experiment

intensityCutoff

The intensity value for accepting the spots intensity value in the experment

datadir

The directory contain data from the experiment

minSumlength

Minimum exceptable number of values to summarize intensity value.

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

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#Summarizes the data in the current directory 
## Not run: 
mySummarizedEset <-workedExampleNotNormalizedData("MyExpt", intensityCutoff=0, datadir=".", minSumlength=0, madAdjust=TRUE)

## End(Not run)