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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

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Microarray analysis software

Microarray Analysis Software

Ricardo Verdugo

ECS 289A – Winter 2003

University of California, Davis


Classes of software
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)


Arraymaker version 2 free for academics
ArrayMaker Version 2(Free for Academics)


Arraymaker version 2 free for academics1
ArrayMaker Version 2(Free for Academics)




Some available software
Some available software

  • Commercial Sources


Some available software1
Some available software

  • Web-based sources


Some available software2
Some available software

  • Freeware sources




Affymetrix data
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



Genestring 5 0
GeneString 5.0

  • Data Normalization


Genestring 5 01
GeneString 5.0

  • Data Clustering


Genestring 5 02
GeneString 5.0

  • 3D Data Visualization


Genestring 5 03
GeneString 5.0

  • Pathway Views


Genestring 5 04
GeneString 5.0

  • Scripting


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