MiChip Parsing and Summarizing Functions

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Documentation for package ‘MiChip’ version 1.63.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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