Preprocessing

Prepare raw microarray data for analysis using background adjustment, normalization, and expression filtering; extensive preprocessing of Affymetrix® and Illumina® data; retrieve probe annotations from library files

Functions

affyrma Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data
affygcrma Perform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data
affyinvarsetnorm Perform rank invariant set normalization on probe intensities from multiple Affymetrix CEL or DAT files
affyprobeaffinities Compute Affymetrix probe affinities from their sequences and MM probe intensities
affysnpintensitysplit Split Affymetrix SNP probe intensity information for alleles A and B
affysnpquartets Create table of SNP probe quartet results for Affymetrix probe set
probesetvalues Create table of Affymetrix probe set intensity values
probesetlookup Look up information for Affymetrix probe set
probesetplot Plot Affymetrix probe set intensity values
probesetlink Display probe set information on NetAffx Web site
probelibraryinfo Create table of probe set library information
rmabackadj Perform background adjustment on Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
rmasummary Calculate gene expression values from Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
gcrma Perform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
gcrmabackadj Perform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
zonebackadj Perform background adjustment on Affymetrix microarray probe-level data using zone-based method
manorm Normalize microarray data
quantilenorm Quantile normalization over multiple arrays
mainvarsetnorm Perform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes
malowess Smooth microarray data using Lowess method
exprprofrange Calculate range of gene expression profiles
exprprofvar Calculate variance of gene expression profiles
geneentropyfilter Remove genes with low entropy expression values
genelowvalfilter Remove gene profiles with low absolute values
generangefilter Remove gene profiles with small profile ranges
genevarfilter Filter genes with small profile variance
maimage Spatial image for microarray data
microplateplot Display visualization of microtiter plate
ilmnbslookup Look up Illumina BeadStudio target (probe) sequence and annotation information
magetfield Extract data from microarray structure
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