Microarray analysis software
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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

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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)


It is worth to take a look

It is worth to take a look


Reading radioactive signal

Reading Radioactive signal


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


Microarray analysis software

ScanAlyse


Scanalyse

ScanAlyse


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=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


Affymetrix data1

Affymetrix Data


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


  • Login