MiChip: MiChip Parsing and Summarizing Functions
Version 1.30.0

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.

AuthorJonathon Blake <blake@embl.de>
Bioconductor views Microarray Preprocessing
Date of publicationNone
MaintainerJonathon Blake <blake@embl.de>
LicenseGPL (>= 2)
Version1.30.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MiChip")

Popular man pages

boxplotDataNoFile: Create Boxplot of data
MiChip: Introduction to the MiChip Package
naOmitMedian: Calculates the median of an array excluding NAs
normalizePerChipMedian: Normalize to median intensity
panelCor: Add Pearson Correlation value to plots
removeUnwantedRows: Removes unwanted rows from data matrix
workedExampleMedianNormalize: Worked Example of MiChip Processing
See all...

All man pages Function index File listing

Man pages

boxplotData: Create Boxplot of data
boxplotDataNoFile: Create Boxplot of data
correctForFlags: Corrects for spots flagged as not present
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...
workedExampleMedianNormalize: Worked Example of MiChip Processing
workedExampleNotNormalizedData: Worked Example of MiChip Processing

Functions

Introduction Man page
MiChip Man page
boxplotData Man page Source code
boxplotDataNoFile Man page Source code
correctForFlags Man page Source code
myForgivingMedian Man page Source code
naOmitMedian Man page Source code
normalizePerChipMedian Man page Source code
outputAnnotatedDataMatrix Man page Source code
panelCor Man page Source code
parseRawData Man page Source code
plotIntensitiesScatter Man page Source code
removeUnwantedRows Man page Source code
returnAnnotatedDataMatrix Man page Source code
setIntensityCutoff Man page Source code
standardRemoveRows Man page Source code
summarizeIntensitiesAsMedian Man page Source code
workedExampleMedianNormalize Man page Source code
workedExampleNotNormalizedData Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/MiChip.R
build
build/vignette.rds
inst
inst/doc
inst/doc/MiChip.R
inst/doc/MiChip.Rnw
inst/doc/MiChip.pdf
inst/extdata
inst/extdata/B_676.gpr
inst/extdata/B_677.gpr
man
man/MiChip.Rd
man/boxplotData.Rd
man/boxplotDataNoFile.Rd
man/correctForFlags.Rd
man/myForgivingMedian.Rd
man/naOmitMedian.Rd
man/normalizePerChipMedian.Rd
man/outputAnnotatedDataMatrix.Rd
man/panelCor.Rd
man/parseRawData.Rd
man/plotIntensitiesScatter.Rd
man/removeUnwantedRows.Rd
man/returnAnnotatedDataMatrix.Rd
man/setIntensityCutoff.Rd
man/standardRemoveRows.Rd
man/summarizeIntensitiesAsMedian.Rd
man/workedExampleMedianNormalize.Rd
man/workedExampleNotNormalizedData.Rd
vignettes
vignettes/MiChip.Rnw
MiChip documentation built on May 20, 2017, 9:56 p.m.