MiChip Parsing and Summarizing Functions


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Documentation for package ‘MiChip’ version 1.22.0

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boxplotData Create Boxplot of data
boxplotDataNoFile Create Boxplot of data
correctForFlags Corrects for spots flagged as not present
Introduction Introduction to the MiChip Package
MiChip Introduction to the MiChip Package
myForgivingMedian Produce Median from Probe Intensity values
naOmitMedian Calculates the median of an array excluding NAs
normalizePerChipMedian Normalize to median intensity
outputAnnotatedDataMatrix Outputs a tab delimited file from an ExpressionSet
panelCor Add Pearson Correlation value to plots
parseRawData Parse raw data files to create an ExpressionSet
plotIntensitiesScatter Plot pairwise intensity scatter
removeUnwantedRows Removes unwanted rows from data matrix
returnAnnotatedDataMatrix returns and annotated data matrix from an ExpressionSet
setIntensityCutoff Sets a cutoff for the lowest intensity value
standardRemoveRows Removes a standard list of features for MiChip processing
summarizeIntensitiesAsMedian Summarizes the probe intensity as median of replicates spotted
workedExampleMedianNormalize Worked Example of MiChip Processing
workedExampleNotNormalizedData Worked Example of MiChip Processing