Modifies the analysis Template
1 2 3 4 5 6 | modifyAnalysis(analysisTemplate, gprDir = gprDir,
analysisPath = analysisPath, normMethod = normMethod, ndups = ndups,
spacing = spacing, minDetectLim = minDetectLim,
subsetByManualControl = subsetByManualControl,
subsetByPMvsMM = subsetByPMvsMM, orderingVar = orderingVar,
addInterestCand = addInterestCand)
|
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 |
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