# MiChip Parsing and Summarizing Functions

## Documentation for package ‘MiChip’ version 1.22.0

- 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