inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.doASCRMAv1.ArrayExplorer.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-4, timestamp=TRUE)



dataSet <- "GSE8605"
chipType <- "Mapping10K_Xba142"

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Tests for setting up CEL sets and locating the CDF file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType, verbose=verbose)
keep <- 1:6
csR <- csR[keep]
print(csR)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Spatial intensity plots
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ae <- ArrayExplorer(csR)
setColorMaps(ae, "sqrt,yellow")
print(ae)
stopifnot(identical(unname(getArrays(ae)), getNames(csR)))
process(ae, verbose=verbose)



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Spatial probe log-ratio plots
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cfR <- getAverageFile(csR, verbose=verbose)
reporter <- SpatialReporter(csR, reference=cfR)
addColorMap(reporter, "log2center,rainbow")
process(reporter, zrange=c(-2,2), verbose=verbose)

ylab <- expression(log[2](y/y[R]))
for (ii in seq_along(csR)) {
  df <- csR[[ii]]

  toPNG(getFullName(df), tags="spatial,rowMedians", width=300, aspectRatio=8/3, {
    plotMargins(reporter, array=ii, ylim=c(-1,1)*0.2, ylab=ylab, margins="rows", rotate=90)
  })

  toPNG(getFullName(df), tags="spatial,colMedians", width=800, aspectRatio=3/8, {
    plotMargins(reporter, array=ii, ylim=c(-1,1)*0.2, ylab=ylab, margins="columns", rotate=0)
  })
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Spatial residual plots test
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
res <- doASCRMAv1(csR, drop=FALSE, verbose=verbose)
plm <- res$plm
print(plm)

# Calculate PLM residuals
rs <- calculateResidualSet(plm, verbose=verbose)
print(rs)

ae <- ArrayExplorer(rs)
setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow"))
print(ae)

# Sanity check
stopifnot(all(getArrays(ae) == getNames(csR)))

process(ae, interleaved="auto", verbose=verbose)