Hivanson Week 13

1. I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
   • The downloaded dataset, as expected, has times (in minutes) 3, 6, 12, 20, 40, 70, and 120, with 3 trials of each time point for CHP and Control yeast.
2. Along with the QA's, I made a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
3. Report on these quality measures:
   • Are all the samples described in the paper in the dataset?
   • Are all the samples in the dataset described in the paper?
4. Come up with consistent column headers that summarize this information
   • For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.
   • Do not use any special characters except for "-" or "_" (e.g., no commas, etc.)
5. Organize the data in a worksheet in an Excel workbook so that:
   • ID (SGD systematic name) is in the first column
   • Data columns are to the right, in increasing chronological order, using the column header pattern you created
   • Treatments are grouped together
   • Replicates are grouped together
6. This information needs to be relayed to the Coder/Designers so that they can design an appropriate expression table.