Color bias adjustment of Illumina Infinium methylaton microarrays using smooth quantile normalization
Add the nuID information to the LumiBatch object
Convert methylation M-value to Beta-value
Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray
Example Illumina Infinium Methylation titration data in MethyLumiM class
Plot the color bias of Illumina Infinium Methylation data in two dimensions
Estimate methylation M-value matrix
Get the control probe Ids
plot the density distribution
Pair plot of an ExpressionSet object
plot the fitting results of gammaFitEM From raw Illumina probe intensities to expression values
Convert methylation Beta-value to M-value
Estimate the background levels of Illumina Infinium methylaton microarrays
Produce GEO Sample Submission File in SOFT format
Between chip normalization of a LumiBatch object
Estimate methylation Beta-value matrix
A summary of colorBias information
Estimated methylation call
plot the Stringency related control probe profiles
Shift and scaling normalization of Illumina Infinium methylation data at probe level
Mapping Illumina TargetID (GeneID) into nuID
plot the cumulative distribution function of a ExpressionSet object
Get the types of the control probes
Plot the mean expression (with standard deviation bar) of different type of control probes
Plot the housekeeping gene expression profile
Produce GEO Platform Submission File in SOFT format
Normalize the Illumina Infinium methylation data
Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization
MAplot of a ExpressionSet object
Example Illumina Expression data in LumiBatch class
A package for preprocessing Illumina microarray data
Estimate the coefficient of variance matrix of LumiBatch object
Read BeadStudio output files in batch
Estimate the detectable probe ratio
Detect the outlier sample (or gene)
produceMethylationGEOSubmissionFile
Produce GEO Sample Submission File of Illumina methylation microarray data in SOFT format
Density plot of a ExpressionSet object
Plot of a ExpressionSet object
boxplot of a ExpressionSet object
Get Illumina Chip Information based on probe identifiers
get the chromosome location information of methylation probes
Fitting a curve with monotonic spline
Matching Illumina IDs to nuID based on Illumina ID mapping library
Mapping nuID into Illumina ProbeID
smoothQuantileNormalization
Smooth quantile normalization
nuID self-identification
Monotonic smooth method
Mapping Illumina ProbeID as nuID
Map nuID to RefSeq ID
Estimate the methylation status of individual methylation sites
Reading Illumina methylation microarray data
Transfer a nuID as a nucleotide sequence
convert the data matrix in the assayData of a ExpressionSet as BigMatrix
visualize the sample relations
Map nuID to Entrez ID
Rank Invariant Normalization
Density plot of a ExpressionSet object
Transfer a nucleotide sequence as a nuID
Estimate and adjust the background levels of Illumina Infinium methylaton microarrays
Matching nuIDs to Illumina IDs based on Illumina ID mapping library
plot the VST (Variance Stabilizing Transform) function
Import Illumina methylation .idat files as an MethyLumiM object
Example Illumina Infinium Methylation data in MethyLumiM class
Read in Illumina expression data
Get control probe information
Transfer the Illumina data to stabilize the variance
Plot the Illumina Infinium methylation color bias in terms of boxplot
normalizeMethylation.quantile
Quantile normalization of Illumina Infinium methylation data at probe level
Background adjustment for Illumina data
produceGEOSampleInfoTemplate
Produce the template of GEO sample information
Inverse VST transform
boxplot,MethyLumiM-method
boxplot of a MethyLumiM object
get the mapping information from nuID to RefSeq ID
Estimate the methylation status by fitting a Gamma mixture model using EM algorithm
Background correction of Illumina Expression data
Adjust background level of Illumina Infinium methylation data
Estimate intensity of Illumina methylation data
Add the control probe data into the controlData slot of LumiBatch object
addControlData2methyLumiM
Add methylation control data to a MethyLumiM object
Class LumiBatch: contain and describe Illumina microarray data
Plot the color bias density plot of Illumina Infinium Methylation data
Mapping nuID into Illumina TargetID
Color bias adjust of Illumina Infinium methylation data
Variance Stabilizing Transformation
Simple Scaling Normalization
Quality control evaluation of the LumiBatch object
Robust Spline Normalization between chips