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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)
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
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