MiChip: MiChip Parsing and Summarizing Functions

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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.

Author
Jonathon Blake <blake@embl.de>
Date of publication
None
Maintainer
Jonathon Blake <blake@embl.de>
License
GPL (>= 2)
Version
1.28.0

View on Bioconductor

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

Files in this package

MiChip/DESCRIPTION
MiChip/NAMESPACE
MiChip/R
MiChip/R/MiChip.R
MiChip/build
MiChip/build/vignette.rds
MiChip/inst
MiChip/inst/doc
MiChip/inst/doc/MiChip.R
MiChip/inst/doc/MiChip.Rnw
MiChip/inst/doc/MiChip.pdf
MiChip/inst/extdata
MiChip/inst/extdata/B_676.gpr
MiChip/inst/extdata/B_677.gpr
MiChip/man
MiChip/man/MiChip.Rd
MiChip/man/boxplotData.Rd
MiChip/man/boxplotDataNoFile.Rd
MiChip/man/correctForFlags.Rd
MiChip/man/myForgivingMedian.Rd
MiChip/man/naOmitMedian.Rd
MiChip/man/normalizePerChipMedian.Rd
MiChip/man/outputAnnotatedDataMatrix.Rd
MiChip/man/panelCor.Rd
MiChip/man/parseRawData.Rd
MiChip/man/plotIntensitiesScatter.Rd
MiChip/man/removeUnwantedRows.Rd
MiChip/man/returnAnnotatedDataMatrix.Rd
MiChip/man/setIntensityCutoff.Rd
MiChip/man/standardRemoveRows.Rd
MiChip/man/summarizeIntensitiesAsMedian.Rd
MiChip/man/workedExampleMedianNormalize.Rd
MiChip/man/workedExampleNotNormalizedData.Rd
MiChip/vignettes
MiChip/vignettes/MiChip.Rnw