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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

affyrmaPerform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data
affygcrmaPerform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data
affyinvarsetnormPerform rank invariant set normalization on probe intensities from multiple Affymetrix CEL or DAT files
affyprobeaffinitiesCompute Affymetrix probe affinities from their sequences and MM probe intensities
affysnpintensitysplitSplit Affymetrix SNP probe intensity information for alleles A and B
affysnpquartetsCreate table of SNP probe quartet results for Affymetrix probe set
probesetvaluesCreate table of Affymetrix probe set intensity values
probesetlookupLook up information for Affymetrix probe set
probesetplotPlot Affymetrix probe set intensity values
probesetlinkDisplay probe set information on NetAffx Web site
probelibraryinfoCreate table of probe set library information
rmabackadjPerform background adjustment on Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
rmasummaryCalculate gene expression values from Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
gcrmaPerform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
gcrmabackadjPerform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
zonebackadjPerform background adjustment on Affymetrix microarray probe-level data using zone-based method
manormNormalize microarray data
quantilenormQuantile normalization over multiple arrays
mainvarsetnormPerform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes
malowessSmooth microarray data using Lowess method
exprprofrangeCalculate range of gene expression profiles
exprprofvarCalculate variance of gene expression profiles
geneentropyfilterRemove genes with low entropy expression values
genelowvalfilterRemove gene profiles with low absolute values
generangefilterRemove gene profiles with small profile ranges
genevarfilterFilter genes with small profile variance
maimageSpatial image for microarray data
microplateplotDisplay visualization of microtiter plate
ilmnbslookupLook up Illumina BeadStudio target (probe) sequence and annotation information
magetfieldExtract data from microarray structure

Topics

Visualizing Microarray Images

Create figures to visualize microarray data and get the data ready for analysis.

Analyzing Gene Expression Profiles

Analyze microarray data for patterns and plot the results.

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