Perform an analysis on the First 1.0 chip
1 2 3 4 5 6 | performAnalysis1_0(gprDir = file.path(getwd(), "../"),
analysisPath = file.path(getwd()), normMethod = "quantile", ndups = 8,
spacing = 1, minDetectLim = 0.15, subsetByManualControl = FALSE,
subsetByPMvsMM = TRUE, orderingVar = "Name",
addInterestCand = c("900000", "20285", "20285_1", "20285_2"),
executeKnitR = TRUE)
|
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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