1. Getting & Using MeV

2. Loading TDMS (tab-delimited text) data

3. Display & Options Lay of the land: Options across top History on left (expand) Expression image on right Info box, right-click options Display Menu Adjustments: Element size (10x10 or 50x10) Color scale (-2 to +2 or other) Color scheme Gene Row labels depends on what you’ve imported with data; common

4. Data Set Notes: Data used in this lab exercise was generated from Affy Mouse chips that were stripped twice. Each chip was rotated among the three conditions. Samples: A1, A2, A3, B1, B2, B3, C1, C2, C3 –A, B, C – chip identifier –1, 2, 3 – uses –++: wild type (normal) A1, B2, C3 –dd: knockout A2, B3, C1 –hfN: hagfish gene A3, B1, C2

5. Analysis (of many, many options) Normalization: Affy data has already been normalized and converted to log2 prior to import Trim/filter: –Adjust Data/Data Filters/Variance Filter Statistical tests: SAM and/or ANOVA –Analysis/SAM/Multiclass (3): ++, dd, hfN –Analysis/ANOVA (3): ++, dd, hfN Hierarchical clustering (HCL) –Pearson Correlation; average linkage

6. Saving Data as Clusters or Txt