Matching Illumina IDs to nuID based on Illumina ID mapping library
Class LumiBatch: contain and describe Illumina microarray data
Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray
Add the control probe data into the controlData slot of LumiBatch object
Add methylation control data to a MethyLumiM object
Add the nuID information to the LumiBatch object
Color bias adjustment of Illumina Infinium methylaton microarrays using smooth quantile normalization
Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization
convert the data matrix in the assayData of a ExpressionSet as BigMatrix
Convert methylation Beta-value to M-value
Estimate and adjust the background levels of Illumina Infinium methylaton microarrays
Plot the Illumina Infinium methylation color bias in terms of boxplot
Estimate intensity of Illumina methylation data
Estimate the coefficient of variance matrix of LumiBatch object
Estimate the background levels of Illumina Infinium methylaton microarrays
Example Illumina Expression data in LumiBatch class
Example Illumina Infinium Methylation data in MethyLumiM class
Example Illumina Infinium Methylation titration data in MethyLumiM class
Estimate the methylation status by fitting a Gamma mixture model using EM algorithm
Get Illumina Chip Information based on probe identifiers
get the chromosome location information of methylation probes
get the mapping information from nuID to RefSeq ID
Transfer a nuID as a nucleotide sequence
Import Illumina methylation .idat files as an MethyLumiM object
A package for preprocessing Illumina microarray data
Background correction of Illumina Expression data
From raw Illumina probe intensities to expression values
Adjust background level of Illumina Infinium methylation data
Color bias adjust of Illumina Infinium methylation data
Normalize the Illumina Infinium methylation data
Reading Illumina methylation microarray data
Estimate the methylation status of individual methylation sites
Between chip normalization of a LumiBatch object
Quality control evaluation of the LumiBatch object
Transfer the Illumina data to stabilize the variance
Convert methylation M-value to Beta-value
Quantile normalization of Illumina Infinium methylation data at probe level
Shift and scaling normalization of Illumina Infinium methylation data at probe level
Matching nuIDs to Illumina IDs based on Illumina ID mapping library
plot the cumulative distribution function of a ExpressionSet object
Plot the color bias density plot of Illumina Infinium Methylation data
Plot the color bias of Illumina Infinium Methylation data in two dimensions
Plot the mean expression (with standard deviation bar) of different type of control probes
plot the fitting results of 'gammaFitEM'
Plot the housekeeping gene expression profile
plot the Stringency related control probe profiles
plot the VST (Variance Stabilizing Transform) function
Produce GEO Platform Submission File in SOFT format
Produce the template of GEO sample information
Produce GEO Sample Submission File in SOFT format
Produce GEO Sample Submission File of Illumina methylation microarray data in SOFT format
Robust Spline Normalization between chips
Transfer a nucleotide sequence as a nuID
Mapping Illumina TargetID (GeneID) into nuID