Microarray Analysis Software - PowerPoint by HC120916153659

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									Microarray Analysis Software

          Ricardo Verdugo

      ECS 289A – Winter 2003
     University of California, Davis
        Classes of software
1.          Array experiment image analysis
     I.       Load image (.SCN , TIFF , others)
     II.      Select channels
     III.     Select parameter
     IV.      Normalization
     V.       Gridding
     VI.      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)
It is worth to take a look
Reading Radioactive signal
         Some 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/              www.ebi.ac.uk/microarray   Hierarchical clustering, k-
Means                                            means and finding nearest
Expression                                       neighbors
Profiler
        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            http://rana.lbl.gov/EisenSoft   T-test, Mann-Whitney test,
Cluster              ware.htm                        SOM, modified Pearson’s
Tree View                                            correlation coefficient
ScanAlyse
ScanAlyse
                                    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
Affymetrix 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

								
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