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

2. 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)

3. ArrayMaker Version 2 (Free for Academics)

9. It is worth to take a look

10. Reading Radioactive signal

11. Some available software Commercial Sources ProgramWeb addressTypes of functions Array Visionwww.imagingresearch.comImage viewing, normalization, data extraction GeneSpring 5.0 www.sigenetics.comt-test, 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

12. Some available software Web-based sources ProgramWeb addressTypes of functions Gene Maths www.applied-maths.comHierarchical clustering, k- means, SOM, PCA, discrimination analysis with or without variance EPCLUST/ Means Expression Profiler www.ebi.ac.uk/microarrayHierarchical clustering, k- means and finding nearest neighbors

13. 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 http://rana.lbl.gov/EisenSoft ware.htm T-test, Mann-Whitney test, SOM, modified Pearson’s correlation coefficient

16. ScanAlyse

18. Affymetrix Data [CEL] Version=3 [HEADER] Cols=640 Rows=640 TotalX=640 TotalY=640 OffsetX=0 OffsetY=0 GridCornerUL=227 235 GridCornerUR=4495 248 GridCornerLR=4462 4514 GridCornerLL=194 4500 Axis-invertX=0 AxisInvertY=0 swapXY=0 DatHeader=[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=Percentile AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004 [INTENSITY] NumberCells=409600 CellHeader=XYMEANSTDVNPIXELS 0 0111.021.3 25 1 010116.51543.4 20 2 0130.0183.6 25 3 09843.01893.8 25 4 072.525.0 20 5 093.012.8 25 6 09556.01746.1 25 7 0105.019.1 20 8 09213.02078.4 25 9 0132.047.5 25 10 09685.31357.6 20 11 0115.0130.3 25 12 09346.01612.0 25 13 0114.027.3 20 14 08730.01991.5 25

19. Affymetrix Data

22. GeneString 5.0 Data Normalization

23. GeneString 5.0 Data Clustering

24. GeneString 5.0 3D Data Visualization

25. GeneString 5.0 Pathway Views

26. GeneString 5.0 Scripting