marray (version 1.50.0)

marrayNorm-class: Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data

Description

This class represents post-normalization intensity data for a batch of cDNA microarrays. A batch of arrays consists of a collection of arrays with the same layout ("marrayLayout"). The class contains slots for the average log-intensities A, the normalized log-ratios M, the location and scale normalization values, the layout of the arrays, and descriptions of the target samples hybridized to the arrays and probe sequences spotted onto the arrays.

Objects from the Class

Objects can be created by calls of the form new('marrayNorm', maA = ...., # Object of class matrix maM = ...., # Object of class matrix maMloc = ...., # Object of class matrix maMscale = ...., # Object of class matrix maW = ...., # Object of class matrix maLayout = ...., # Object of class marrayLayout maGnames = ...., # Object of class marrayInfo maTargets = ...., # Object of class marrayInfo maNotes = ...., # Object of class character maNormCall = ...., # Object of class call )

References

S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.

See Also

marrayLayout, marrayRaw, marrayInfo

Examples

# Examples use swirl dataset, for description type ? swirl

data(swirl)

# Median normalization
mnorm<-maNorm(swirl[,2:3],norm="m")

# Object of class marrayNorm for the second and third swirl arrays
mnorm

# Function call
maNormCall(mnorm)

#  Object of class marrayInfo -- Probe sequences
maGnames(mnorm)

#  Object of class marrayInfo -- Target samples
 maTargets(mnorm)

# Density plot of log-ratios M for third array
plot(density(maM(mnorm[,2])), lwd=2, col=2, main="Density plots of log-ratios M")
lines(density(maM(swirl[,3])), lwd=2)
abline(v=0)
legend(2,1,c("Pre-normalization","Post-normalization"))