Microarray Analysis Software

naivenorthΤεχνίτη Νοημοσύνη και Ρομποτική

8 Νοε 2013 (πριν από 4 χρόνια και 5 μέρες)

71 εμφανίσεις

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