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MiChip (version 1.26.0)

MiChip Parsing and Summarizing Functions

Description

This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.

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Version

Version

1.26.0

License

GPL (>= 2)

Maintainer

Jonathon Blake

Last Published

February 15th, 2017

Functions in MiChip (1.26.0)

boxplotDataNoFile

Create Boxplot of data
boxplotData

Create Boxplot of data
MiChip

Introduction to the MiChip Package
correctForFlags

Corrects for spots flagged as not present
returnAnnotatedDataMatrix

returns and annotated data matrix from an ExpressionSet
myForgivingMedian

Produce Median from Probe Intensity values
parseRawData

Parse raw data files to create an ExpressionSet
plotIntensitiesScatter

Plot pairwise intensity scatter
naOmitMedian

Calculates the median of an array excluding NAs
standardRemoveRows

Removes a standard list of features for MiChip processing
normalizePerChipMedian

Normalize to median intensity
outputAnnotatedDataMatrix

Outputs a tab delimited file from an ExpressionSet
panelCor

Add Pearson Correlation value to plots
removeUnwantedRows

Removes unwanted rows from data matrix
workedExampleMedianNormalize

Worked Example of MiChip Processing
setIntensityCutoff

Sets a cutoff for the lowest intensity value
workedExampleNotNormalizedData

Worked Example of MiChip Processing
summarizeIntensitiesAsMedian

Summarizes the probe intensity as median of replicates spotted