Preprocessing
Process microarray data using background adjustment, normalization, and expression filtering. You can perform extensive preprocessing of Affymetrix® and Illumina® data and retrieve probe annotations from library files.
Functions
Robust Multi-Array Average Procedure
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 |
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 |
probelibraryinfo | Create table of probe set library information |
Background Adjustment
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 |
Normalization
manorm | Normalize microarray data |
quantilenorm | Perform 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 |
Gene Filtering
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 |
Visualization
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 |
Featured Examples
Preprocessing Affymetrix Microarray Data at the Probe Level
Use MATLAB® and Bioinformatics Toolbox™ for preprocessing Affymetrix® oligonucleotide microarray probe-level data with two preprocessing techniques, Robust Multi-array Average (RMA) and GC Robust Multi-array Average (GCRMA).
MATLAB 명령
다음 MATLAB 명령에 해당하는 링크를 클릭했습니다.
명령을 실행하려면 MATLAB 명령 창에 입력하십시오. 웹 브라우저는 MATLAB 명령을 지원하지 않습니다.
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