tests/test06-pipeline.R

In PreProcess: Basic Functions for Pre-Processing Microarrays

# pipeline-test
library(PreProcess)

suppressWarnings( RNGversion("3.5.3") )
set.seed(147745)
# simulate a moderately realistic looking microarray
nc <- 100
nr <- 100
v <- rexp(nc*nr, 1/1000)
b <- rnorm(nc*nr, 80, 10)
s <- sapply(v-b, max, 1)
ct <- ChannelType('user', 'random', nc, nr,  'fake')
subbed <- Channel(name='fraud', parent='', type=ct, vec=s)
rm(ct, nc, nr, v, b, s)		# clean some stuff

# example of standard data processing
processed <- process(subbed, PIPELINE.STANDARD)

summary(processed)

par(mfrow=c(2,1))
plot(processed)
hist(processed)

par(mfrow=c(1,1))
image(processed)

rm(subbed, processed)