Microarray Analysis Software Ricardo Verdugo ECS 289A – Winter 2003 University of California, Davis Ricardo Verdugo ECS 289A – Winter 2003 University of.

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Presentation transcript:

Microarray Analysis Software Ricardo Verdugo ECS 289A – Winter 2003 University of California, Davis Ricardo Verdugo ECS 289A – Winter 2003 University of California, Davis

Classes of software 1.Array experiment image analysis I.Load image (.SCN, TIFF, others) II.Select channels III.Select parameter IV.Normalization V.Gridding VI.Reading 2.Statistical analysis of raw data ???? 3.Discovery tools (you name it) 1.Array experiment image analysis I.Load image (.SCN, TIFF, others) II.Select channels III.Select parameter IV.Normalization V.Gridding VI.Reading 2.Statistical analysis of raw data ???? 3.Discovery tools (you name it)

ArrayMaker Version 2 (Free for Academics)

It is worth to take a look

Reading Radioactive signal

Some available software Commercial Sources ProgramWeb addressTypes of functions Array Visionwww.imagingresearch.comImage viewing, normalization, data extraction GeneSpring hierarchical clustering, k-means, SOM, PCA, class predictor, experiment tree Data Mining Tool (DMT) 3.0www.affymetrix.xomT-test, Mann-Whitney test, SOM, modified Pearson’s correlation coefficient GeneSight 3www.biodiscovery.comt-test, k-means, hierarchical clustering, SOM, PCA, pattern similarity search, non-linear normalization

Some available software Web-based sources ProgramWeb addressTypes of functions Gene Maths clustering, k- means, SOM, PCA, discrimination analysis with or without variance EPCLUST/ Means Expression Profiler clustering, k- means and finding nearest neighbors

Some available software Freeware sources ProgramWeb addressTypes of functions J-Expresswww.molmine.comHierarchical clustering, k- means, PCA, SOM, profile similarity search ScanAlyze Cluster Tree View ware.htm T-test, Mann-Whitney test, SOM, modified Pearson’s correlation coefficient

ScanAlyse

Affymetrix Data [CEL] Version=3 [HEADER] Cols=640 Rows=640 TotalX=640 TotalY=640 OffsetX=0 OffsetY=0 GridCornerUL= GridCornerUR= GridCornerLR= GridCornerLL= Axis-invertX=0 AxisInvertY=0 swapXY=0 DatHeader=[ ] PoolA_Mg74AV2:CLS=4733 RWS=4733 XIN=3 YIN=3 VE= /21/02 12:20:00 MG_U74Av2.1sq Algorithm=Percentile AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004 [INTENSITY] NumberCells= CellHeader=XYMEANSTDVNPIXELS

Affymetrix Data

GeneString 5.0 Data Normalization

GeneString 5.0 Data Clustering

GeneString 5.0 3D Data Visualization

GeneString 5.0 Pathway Views

GeneString 5.0 Scripting