modifyAnalysis: Modifies the analysis Template

Description Usage Arguments

Description

Modifies the analysis Template

Usage

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modifyAnalysis(analysisTemplate, gprDir = gprDir,
  analysisPath = analysisPath, normMethod = normMethod, ndups = ndups,
  spacing = spacing, minDetectLim = minDetectLim,
  subsetByManualControl = subsetByManualControl,
  subsetByPMvsMM = subsetByPMvsMM, orderingVar = orderingVar,
  addInterestCand = addInterestCand)

Arguments

analysisTemplate

Analysis template (chip version)

gprDir

directory of gpr file

analysisPath

path were the html and quality control files should be written

normMethod

normalization method one wants to use (quantile or vsn)

ndups

number of duplicated spots on the chip

spacing

spacing between the duplicated spots

minDetectLim

minimum detection limit obtained from self-self hybridization experiment

subsetByManualControl

if data should be subsetted by spike in control (Chip 1 -> no spike in controls)

subsetByPMvsMM

if data should be subsetted by PM > MM condition

orderingVar

By which variable should spot ordering occur

addInterestCand

Candidate IDs that are added as labels in the plots and in the table


SimonSchafferer/custom-neuro-ncRNA-microarray documentation built on May 9, 2019, 1:45 p.m.