microarray analysis software
DESCRIPTION
Microarray Analysis Software. Ricardo Verdugo ECS 289A – Winter 2003 University of California, Davis. Classes of software. Array experiment image analysis Load image (.SCN , TIFF , others) Select channels Select parameter Normalization Gridding Reading - PowerPoint PPT PresentationTRANSCRIPT
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Microarray Analysis SoftwareMicroarray Analysis Software
Ricardo Verdugo
ECS 289A – Winter 2003
University of California, Davis
Ricardo Verdugo
ECS 289A – Winter 2003
University of California, Davis
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Classes of softwareClasses of software
1. Array experiment image analysisI. Load image (.SCN , TIFF , others)II. Select channelsIII. Select parameterIV. NormalizationV. GriddingVI. Reading
2. Statistical analysis of raw data ????
3. Discovery tools (you name it)
1. Array experiment image analysisI. Load image (.SCN , TIFF , others)II. Select channelsIII. Select parameterIV. NormalizationV. GriddingVI. Reading
2. Statistical analysis of raw data ????
3. Discovery tools (you name it)
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ArrayMaker Version 2(Free for Academics)
ArrayMaker Version 2(Free for Academics)
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ArrayMaker Version 2(Free for Academics)ArrayMaker Version 2(Free for Academics)
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It is worth to take a look
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Reading Radioactive signalReading Radioactive signal
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Some available softwareSome 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 Pearson’s 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 Pearson’s correlation coefficient
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ScanAlyseScanAlyse
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ScanAlyseScanAlyse
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Affymetrix DataAffymetrix Data[CEL]Version=3
[HEADER]Cols=640Rows=640TotalX=640TotalY=640OffsetX=0OffsetY=0GridCornerUL=227 235GridCornerUR=4495 248GridCornerLR=4462 4514GridCornerLL=194 4500Axis-invertX=0AxisInvertY=0swapXY=0DatHeader=[0..46136] PoolA_Mg74AV2:CLS=4733 RWS=4733 XIN=3 YIN=3 VE=17 2.0 03/21/02 12:20:00 MG_U74Av2.1sq Algorithm=PercentileAlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004
[INTENSITY]NumberCells=409600CellHeader=X Y MEAN STDV NPIXELS 0 0 111.0 21.3 25 1 0 10116.5 1543.4 20 2 0 130.0 183.6 25 3 0 9843.0 1893.8 25 4 0 72.5 25.0 20 5 0 93.0 12.8 25 6 0 9556.0 1746.1 25 7 0 105.0 19.1 20 8 0 9213.0 2078.4 25 9 0 132.0 47.5 25 10 0 9685.3 1357.6 20 11 0 115.0 130.3 25 12 0 9346.0 1612.0 25 13 0 114.0 27.3 20 14 0 8730.0 1991.5 25
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Affymetrix DataAffymetrix 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