yaqcaffy (version 1.32.0)

reprodPlot: Plot human whole genome GeneChips reproductibility

Description

Compares Affymetrix Human Genome U133 Plus 2.0 Arrays to a subset of the MAQC arrays for a RNA reference.

Usage

reprodPlot(userAffyBatchObject,ref, normalize=c("rma","gcrma","mas5","none"), main="MAQC reference reproducibility", cex,...)

Arguments

userAffyBatchObject

a set of Human Genomue U133 Plus 2.0 arrays provided as an AffBatch object,

ref

a string ("refA", "refB", "refC", or "refD") defining the RNA reference to compare the userAffyBatchObject to,

normalize

a string defining the algorithm used for data normalization: rma (default) for RMA (as imlplemented in the affy library), gcrma for GCRMA (as imlplemented in the gcrma library), mas5 for MAS5 (as imlplemented in the affy library) or 'none' for no normalization,

main

an overall title for the plot,

cex

size of text on the plot,

...

other arguments.

Value

Details

The plot shows all the pairwise scatterplots (plotted with graphics)'s smoothScatter function) with Pearson's correlation factor and MAplots (plotted with affy's ma.plot function). The subset of the MAQC arrays are 1 randomly chosen .CEL file out of the 5 replicates for the 6 different test site.

Examples

 ## Not run: 
#    ## loading data
#    library(MAQCsubsetAFX)
#    data(refB)
#    d<-refB[,1]
#    ## testing the reproductibility against ref A
#    reprodPlot(d,"refA",normalize="rma")
#  ## End(Not run)