bas {OLIN}R Documentation

Between-array scaling

Description

This function performs an between-array scaling

Usage

bas(obj,mode="var")

Arguments

obj object of “marrayNorm”
mode mode of scaling. Default option is scaling of arrays to have the same within-array variance of logged ratios (var). Alternatively, mad qq can be used (see details)

Details

The function bsv adjust the scale of logged ratios (M=(log2(Ch2)-log2(Ch1))) between the different arrays stored in obj.

Following schemes (mode) are implemented:

Note

Between-array scaling should only be performed if it can be assumed that the different arrays have a similar distribution of logged ratios. This has to be check on a case-by-case basis. Caution should be taken in the interpretation of results for arrays hybridised with biologically divergent samples, if between-array scaling is applied.

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

References

Bolstad et al., A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19: 185-193, 2003

See Also

marrayNorm,var,mad

Examples


# DISTRIBUTION OF M BEFORE SCALING
data(sw.olin)

col <- c("red","blue","green","orange")
M <- maM(sw.olin)

plot(density(M[,4]),col=col[4],xlim=c(-2,2))
for (i in 1:3){
  lines(density(M[,i]),col=col[i])
}

# SCALING AND VISUALISATION  
sw.olin.s <- bas(sw.olin,mode="var")
  
M <- maM(sw.olin.s)

plot(density(M[,4]),col=col[4],xlim=c(-2,2))
for (i in 1:3){
  lines(density(M[,i]),col=col[i])
}


[Package OLIN version 1.3.2 Index]