Docstoc

Slide 1 - Institute for Genome Sciences and Policy

Document Sample
Slide 1 - Institute for Genome Sciences and Policy Powered By Docstoc
					    Data Analysis:
General Workflow &
  Analysis Options
    Duke Microarray Core Facility
               Zhengzheng Wei
                      Nov. 2006
Overall Workflow and Analysis
Options
   Normalization (Lowess, RMA, MAS5, Quantile etc.)
   Outlier Sample Removal (unsupervised hierarchical clustering, PCA)
   Quality Control Filtering (Filter on Flag, Expression, Error etc.)
   Gene Selection (ANOVA, Fold Change, SAM, Golub Method, Fisher
    Exact Test, Condition Correlation etc.)
   Clustering (unsupervised hierarchical clustering, supervised hierarchical
    clustering, k-means clustering)
   Gene annotations, Genelist Correlation, Venn Diagram For Genelists
   Gene Ontology Analysis (GATHER, GeneSpring Gene Ontology)
   Class Prediction (Support Vector Machine, K-nearest neighbor, PAM)
   Pathway Analysis (MetaCore, KEGG Pathways)
   Web hosting of Experiment Data
 Principle Component Analysis




Back to Table of Content
ANOVA: Analysis of Variance




Back to Table of Content      Next
  Pairwise comparison: Volcano
  Plot (ANOVA + Fold Change)




Back to Table of Content
 Venn Diagram: Union and
 intersection of Genelists




Back to Table of Content
  Unsupervised Hierarchical Clustering




Back to Table of Content
Supervised Hierarchical Clustering

                           50         1000
      0                         200




Back to Table of Content
K-Means Clustering




Back to Table of Content
Scatter plot




Back to Table of Content
  Class Prediction: SVM
  (Support Vector Machine)
     1.5
     1.0
                                   0   M argin



     0.5
     0.0
              control         50 cGy          200 cGy       1000 cGy
    -0.5
    -1.0
    -1.5
    -2.0                              Data 1
    1.5
                                                                           c ontrol
    1.0
                                                                           50 c Gy
    0.5                                                                    200 c Gy
    0.0                                Data 1                              1000 c Gy
              control         50 cGy         200 cGy        1000 cGy
     1.5
   -0.5
                                  50 margin                                 c ontrol
     1.0
   -1.0                                                                     50 c Gy
     0.5
   -1.5                                                                     200 c Gy
     0.0
   -2.0
                          200 M argin                                       1000 c Gy
                control        50 cGy          200 cGy          1000 cGy
    1.5
    -0.5
                                      50 margin                            c ontrol
    1.0
    -1.0                                                                   50 c Gy
    0.5
    -1.5                                                                   200 c Gy
    0.0
    -2.0                                                                   1000 c Gy
                               y




                                                 y
                 l




                                                                 y
   -0.5
                o




                              G




                                               G




                                                             G
              tr




                              c




                                             c




                                                            c
            n




                          0




                                          0




                                                           0
           o




                          5




                                         0




                                                        0
          c




   -1.0
                                         2




                                                       0
                                                       1
   -1.5
   -2.0                   1000 M argin
    1.5
                                                                           c ontrol
    1.0
                                                                           50 c Gy
    0.5                                                                    200 c Gy
    0.0                                                                    1000 c Gy
                                  y




                                                   y
                 l




                                                                  y
   -0.5
                o




                              G




                                               G




                                                                 G
              tr




                              c




                                              c




                                                                c
            n




                          0




                                           0




                                                            0
           o




                          5




                                          0




                                                            0
          c




   -1.0
                                         2




                                                           0
                                                       1

   -1.5
   -2.0




Back to Table of Content
  Class Prediction: PAM (Prediction
  Analysis for Microarrays )




Back to Table of Content
  Gene Annotations




Back to Table of Content
  Gene Ontology: GATHER




Back to Table of Content
  Gene Ontology: Genespring (1)
  Table with P-value




Back to Table of Content          Next
  Gene Ontology: Genespring
  (2) Pie Chart




Back to Table of Content      Next
  Gene Ontology: Genespring
  (3) split window view




Back to Table of Content
  Web Page Hosting of
  Expression Data




Back to Table of Content

				
DOCUMENT INFO