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:
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. |
The plot shows all the pairwise scatterplots (plotted with
geneplotter)'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)