Microarray Analysis SoftwareMicroarray Analysis Software

Ricardo Verdugo

ECS 289A – Winter 2003

University of California, Davis

Ricardo Verdugo

ECS 289A – Winter 2003

University of California, Davis

Classes of softwareClasses of software

1. Array experiment image analysisI. Load image (.SCN , TIFF , others)II. Select channelsIII. Select parameterIV. NormalizationV. GriddingVI. Reading

2. Statistical analysis of raw data ????

3. Discovery tools (you name it)

1. Array experiment image analysisI. Load image (.SCN , TIFF , others)II. Select channelsIII. Select parameterIV. NormalizationV. GriddingVI. Reading

2. Statistical analysis of raw data ????

3. Discovery tools (you name it)

ArrayMaker Version 2(Free for Academics)

ArrayMaker Version 2(Free for Academics)

ArrayMaker Version 2(Free for Academics)ArrayMaker Version 2(Free for Academics)

It is worth to take a look

Reading Radioactive signalReading Radioactive signal

Some available softwareSome available software

• Commercial Sources

Program Web address Types of functions

Array Vision www.imagingresearch.com Image viewing, normalization, data extraction

GeneSpring 5.0 www.sigenetics.com t-test, hierarchical clustering, k-means, SOM, PCA, class predictor, experiment tree

Data Mining Tool (DMT) 3.0 www.affymetrix.xom T-test, Mann-Whitney test, SOM, modified Pearson’s correlation coefficient

GeneSight 3 www.biodiscovery.com t-test, k-means, hierarchical clustering, SOM, PCA, pattern similarity search, non-linear normalization

Some available software

• Web-based sources

Program Web address Types of functions

Gene Maths www.applied-maths.com Hierarchical clustering, k-means, SOM, PCA, discrimination analysis with or without variance

EPCLUST/

Means

Expression

Profiler

www.ebi.ac.uk/microarray Hierarchical clustering, k-means and finding nearest neighbors

Some available software

• Freeware sources

Program Web address Types of functions

J-Express www.molmine.com Hierarchical clustering, k-means, PCA, SOM, profile similarity search

ScanAlyze

Cluster

Tree View

http://rana.lbl.gov/EisenSoftware.htm

T-test, Mann-Whitney test, SOM, modified Pearson’s correlation coefficient

ScanAlyseScanAlyse

ScanAlyseScanAlyse

Affymetrix DataAffymetrix Data[CEL]Version=3

[HEADER]Cols=640Rows=640TotalX=640TotalY=640OffsetX=0OffsetY=0GridCornerUL=227 235GridCornerUR=4495 248GridCornerLR=4462 4514GridCornerLL=194 4500Axis-invertX=0AxisInvertY=0swapXY=0DatHeader=[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=PercentileAlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004

[INTENSITY]NumberCells=409600CellHeader=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

Affymetrix DataAffymetrix Data

GeneString 5.0

• Data Normalization

GeneString 5.0

• Data Clustering

GeneString 5.0

• 3D Data Visualization

GeneString 5.0

• Pathway Views

GeneString 5.0

• Scripting