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Getting & Using MeV

Getting & Using MeV. Loading TDMS (tab-delimited text) data. 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)

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Getting & Using MeV

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  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

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