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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

affyrma 性能orm Robust Multi-array Average (RMA) procedure onAffymetrixmicroarray probe-level data
affygcrma 性能orm GC Robust Multi-array Average (GCRMA) procedure onAffymetrixmicroarray probe-level data
affyinvarsetnorm 性能orm rank invariant set normalization on probe intensities from multipleAffymetrixCEL or DAT files
affyprobeaffinities ComputeAffymetrixprobe affinities from their sequences and MM probe intensities
affysnpintensitysplit SplitAffymetrixSNP probe intensity information for alleles A and B
affysnpquartets 创建表的SNP探测四方的结果forAffymetrixprobe set
probesetvalues Create table ofAffymetrixprobe set intensity values
probesetlookup Look up information forAffymetrixprobe set
probesetplot PlotAffymetrixprobe set intensity values
probesetlink Display probe set information onNetAffxWeb site
probelibraryinfo Create table of probe set library information
rmabackadj 性能orm background adjustment onAffymetrixmicroarray probe-level data using Robust Multi-array Average (RMA) procedure
rmasummary Calculate gene expression values fromAffymetrixmicroarray probe-level data using Robust Multi-array Average (RMA) procedure
gcrma 性能orm GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization onAffymetrixmicroarray probe-level data
gcrmabackadj 性能orm GC Robust Multi-array Average (GCRMA) background adjustment onAffymetrixmicroarray probe-level data using sequence information
zonebackadj 性能orm background adjustment onAffymetrixmicroarray probe-level data using zone-based method
manorm Normalize microarray data
quantilenorm Quantile normalization over multiple arrays
mainvarsetnorm 性能orm 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 upIlluminaBeadStudiotarget (probe) sequence and annotation information
magetfield Extract data from microarray structure