genArise (version 1.48.0)

Zscore: Z-scores for identifying differential expression

Description

This function identify differential expressed genes by calculating an intensity-dependent Z-score. This function use a sliding window to calculate the mean and standard deviation within a window surrounding each data point, and define a Z-score where Z measures the number of standard deviations a data point is from the mean.

Usage

Zscore(spot.object,type,window.size)

Arguments

spot.object

A spot object

type

Type of analysis: "ri" is for a R-I analysis and "ma" is for M-A analysis

window.size

Size of the sliding window

Value

A dataSet object with attributes Cy3, Cy5, Id, Z-score.

Examples

data(Simon)
# Background Correction
c.spot <- bg.correct(Simon)
#Normalized data
n.spot <- grid.norm(c.spot,23,24)
#Filter spot
f.spot <- filter.spot(n.spot)
#Replicate filtering
u.spot <- spotUnique(f.spot)
#Zscore analysis
s.spot <- Zscore(u.spot)