reprodPlot {yaqcaffy} | R Documentation |
Compares Affymetrix Human Genome U133 Plus 2.0 Arrays to a subset of the MAQC arrays for a RNA reference.
reprodPlot(userAffyBatchObject,ref, normalize=c("rma","gcrma","mas5","none"), main="MAQC reference reproducibility", cex,...)
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:
|
main |
an overall title for the plot, |
cex |
size of text on the plot, |
... |
other arguments. |
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.
Outputs a graph on the available graphical device
Laurent Gatto
## 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)