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Advanced Microarray Analysis Techniques and Software Applications for Data Interpretation

This comprehensive guide by Ricardo Verdugo from the University of California, Davis, covers in-depth microarray analysis software tools and techniques. It addresses image analysis, data normalization, channel selection, and statistical analysis of raw data. The guide introduces various software options, including ArrayMaker Version 2 (free for academics) and ScanAlyse, along with web-based and freeware alternatives for data analysis. It also touches on advanced functionalities like 3D visualization and data clustering, providing resources to enhance microarray data interpretation.

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Advanced Microarray Analysis Techniques and Software Applications for Data Interpretation

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

  2. 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)

  3. ArrayMaker Version 2(Free for Academics)

  4. ArrayMaker Version 2(Free for Academics)

  5. It is worth to take a look

  6. Reading Radioactive signal

  7. Some available software • Commercial Sources

  8. Some available software • Web-based sources

  9. Some available software • Freeware sources

  10. ScanAlyse

  11. ScanAlyse

  12. 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=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

  13. Affymetrix Data

  14. GeneString 5.0 • Data Normalization

  15. GeneString 5.0 • Data Clustering

  16. GeneString 5.0 • 3D Data Visualization

  17. GeneString 5.0 • Pathway Views

  18. GeneString 5.0 • Scripting

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