Search
Experiment
Probe Set
Website
for
News
Data Access
Probe Set Info
Analysis & Viz.
Database Overview
Tools
My BarleyBase
Feedback
Hello! Guest! Please
Login
or
Register
!
Log Out
Setup Data Analysis Parameters
Step 1. Choose a Gene List for Analysis:
Gene List Management
1. guest_D3, untitled, from TA1, mas, GO2Expression--Gene Ontology to Gene List Filter , 0 genes, 2006-02-21 16:39:52
2. guest_D2, untitled, from BB1, mas, Absolute Value Filter, 695 genes, 2005-08-18 12:27:45
Step 2. Select an Analysis Method from the List:
1. 1. Hierarchical Clustering
2. 2. K-medoids (PAM) and K-means Partitioning
3. 3. Self-Organization Map (SOM)
4. 4. Principal Components Analysis (PCA)
5. 5. Sammon's Non-Linear Mapping
Step 3. Setup Analysis and Run:
1. Hierarchical Clustering Settings:
Help
First, decide if do clustering.
Hierarchical Clustering:
Cluster filtered genes
Cluster samples with filtered genes
Log2 transform data if not yet, for example the MAS5.0 estimations.
Mean-center log2 transformed data so that each row has mean 0.
Select a clustering method:
single linkage
average linkage
complete linkage
ward
mcquitty
median
centroid
Select a distance method:
Correlation - Centered Pearson
Non-Centered Pearson
Euclidean Distance
maximum
manhattan
canberra
The number of clusters to use (may based on preliminary output) is
Heapmap color spectrum:
Green (low) and Red (high)
Blue (low) and Yellow (high)
Define the Treatments to be Included in Analysis
Factor1:
1. All Levels of factor genotype
2. Wheat (BB1-H1/S1)
3. Barley (Mla1-5874-0hai)
Experiment Design Details:
Hybridization
T
REP
Factor:
genotype
File_Name
Sample_ID & Name
1
TA1_H1
1
1
Wheat (BB1-H1/S1)
0502-1_0308-1_BB1_H3_Wheat
TA1_S1
0308-1
2
TA1_H2
2
1
Barley (Mla1-5874-0hai)
0502-2_0449-35
TA1_S2
0449-35
T= Treatment; REP = Replicate
Copyright@2001-2005 The
BarleyBase Group
All rights reserved.
For problems with the webpages, contact
barleybasewebmaster