Microarray Analysis Software

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Microarray Analysis Software

• Ricardo Verdugo
• ECS 289A Winter 2003
• University of California, Davis

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Classes of software

• Array experiment image analysis
• Load image (.SCN , TIFF , others)
• Select channels
• Select parameter
• Normalization
• Gridding
• Reading
• Statistical analysis of raw data ????
• Discovery tools (you name it)

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ArrayMaker Version 2(Free for Academics)
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ArrayMaker Version 2(Free for Academics)
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It is worth to take a look
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Reading Radioactive signal
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Some available software

• Commercial Sources

Program Web address Types of functions
Array Vision www.imagingresearch.com Image viewing, normalization, data extraction
GeneSpring 5.0 www.sigenetics.com t-test, hierarchical clustering, k-means, SOM, PCA, class predictor, experiment tree
Data Mining Tool (DMT) 3.0 www.affymetrix.xom T-test, Mann-Whitney test, SOM, modified Pearsons correlation coefficient
GeneSight 3 www.biodiscovery.com t-test, k-means, hierarchical clustering, SOM, PCA, pattern similarity search, non-linear normalization
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Some available software

• Web-based sources

Program Web address Types of functions
Gene Maths www.applied-maths.com Hierarchical clustering, k-means, SOM, PCA, discrimination analysis with or without variance
EPCLUST/ Means Expression Profiler www.ebi.ac.uk/microarray Hierarchical clustering, k-means and finding nearest neighbors
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Some available software

• Freeware sources

Program Web address Types of functions
J-Express www.molmine.com Hierarchical clustering, k-means, PCA, SOM, profile similarity search
ScanAlyze Cluster Tree View http//rana.lbl.gov/EisenSoftware.htm T-test, Mann-Whitney test, SOM, modified Pearsons correlation coefficient
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ScanAlyse
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ScanAlyse
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Affymetrix Data

• CEL
• Version3
• HEADER
• Cols640
• Rows640
• TotalX640
• TotalY640
• OffsetX0
• OffsetY0
• GridCornerUL227 235
• GridCornerUR4495 248
• GridCornerLR4462 4514
• GridCornerLL194 4500
• Axis-invertX0
• AxisInvertY0
• swapXY0
• DatHeader0..46136 PoolA_Mg74AV2CLS4733
  RWS4733 XIN3 YIN3 VE17 2.0 03/21/02
  122000
• MG_U74Av2.1sq

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Affymetrix Data
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GeneString 5.0

• Data Normalization

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GeneString 5.0

• Data Clustering

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GeneString 5.0

• 3D Data Visualization

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GeneString 5.0

• Pathway Views

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GeneString 5.0

• Scripting