Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Migration of unmigrated content due to installation of a new plugin

...

Panel
borderColor#ccc
bgColor#c0c0c0
titleBGColor1
borderStyledashed
title*Sample session*
borderStyledashed

## load cellHTS2 and set directory for sample session
library('cellHTS2')
datadir <- system.file("KcViab", package = "cellHTS2")

## read screen description and the result file index
x = readPlateList("Platelist.txt", name="KcViab", path=datadir)

## add plate configuration and screen log
x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt", path=datadir)

## normalize results
xn = normalizePlates(x, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")

## score and summarize replicates
xsc = scoreReplicates(xn, sign="-", method="zscore")
xsc = summarizeReplicates(xsc, summary="mean")

## add reagent and target annotation
xsc = annotate(xsc, geneIDFile="GeneIDs_Dm_HFA_1.1.txt", path=datadir)

## save the data object for further use
save(xsc, file=paste("KcViab", ".rda", sep=""))

## create the HTML linked (web) report
out = writeReport(raw=x, normalized=xn,outdir=tempdir(), scored=xsc, force=TRUE, map=TRUE, plotPlateArgs = TRUE, imageScreenArgs=list(zrange=c(-4,8)))

## open HTML report
browseURL(out)

...

Panel
borderColor#ccc
bgColor#c0c0c0
titleBGColor1
borderStyledashed
title*Install*
borderStyledashed

>source('http://www.bioconductor.org/biocLite.R')
>biocLite('cellHTS2')

...