Kzebrows Week 11

Guild Meeting 10/11: GenMAPP Users

1. Experimental design (for sure do by next week)
   • Treatment vs. control
   • Biological vs. technical replicates: which one and how many
     • Biological replicates: independent samples
     • Technical replicates: if at any point sample is split into two and treated differently
     • NOTE: should be able to find # chips or microarrays (a combo of the above should add up to this)
   • dye swaps: green and red dye behave differently in experiments
     • Figure out how many dye swaps occurred (best is even, but they could have done half and half and swapped it or used technical replicates)
   • Flow chart
2. Sample and data relationships: match each chip/filename with a sample. One file should correspond to one chip. (look at by next week)
   • raw.zip should have the files in it
   • sdrf.txt (Sample Data Relationship File) spreadsheet
   • NOTE: Double-check with Dr. Dahlquist
3. Create compiled raw data file with ID, sample log 2 fold, sample log size, etc.