Microarray Analysis Software

naivenorthAI and Robotics

Nov 8, 2013 (3 years and 11 months ago)

71 views

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/

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/EisenSoft
ware.htm

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