Download - Microarray Analysis Software
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