1 / 26

Microarray Analysis Software

This document provides an in-depth overview of essential software for microarray analysis, especially useful for research and academic purposes. It covers key features like image analysis, data normalization, statistical analysis, and data visualization tools. Users can explore various software options from commercial, web-based, and freeware sources, including ArrayMaker Version 2, ScanAlyse, and GeneString 5.0. The guide aims to equip researchers with knowledge on tools that facilitate image loading, parameter selection, statistical analysis, and data clustering, enhancing their microarray data processing capabilities.

willis
Télécharger la présentation

Microarray Analysis Software

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related