Microarray analysis exercises 3 - with R

WIBR Microarray Analysis Course - 2007

Starting Data    

Class 3 exercises

Part VI. Visualizing all the data

  1. You may try any combination of these graphing techniques. Global visualization of an experiment can be helpful for designing subsequent analysis and for quality control.
  2. Start by reading the output of your analysis from the first class
    all.data = read.delim("Microarray_Analysis_data_1_SOLUTION.txt")
  3. Intensity scatterplot (sample)
  4. R-I (M-A) plot (sample)
  5. volcano plot (sample)

Part VII. Functional analysis

  1. Annotation (Excel and web tools)
  2. Comparing two lists
  3. Genome mapping of one gene or a set of genes
  4. Promoter extraction
  5. Identifying potential transcription factor binding sites with TRANSFAC
  6. Gene Ontology analysis
  7. Pathway analysis (KEGG)
  8. Motif finding (Meme)
  9. Comparisons to other expression data

WIBR Microarray Analysis Course - 2007