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?
     • As described above, the samples listed in the paper were all present in the dataset.
   • Are all the samples in the dataset described in the paper?
     • Yes, but it is worth noting that the researchers stated that timepoints greater than or equal to 40 minutes were not analyzed in their paper, as they grew their yeast for too long and they exhibited some other, nonoxidative stress responses.
4. We came up with consistent column headers that summarize this information
   • CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
5. I ensured the data were organized in a worksheet in an Excel workbook so that:
   • ID (SGD systematic name) was in the first column
   • Data columns were to the right, in increasing chronological order, using the column header pattern we created
   • Treatments are grouped together
   • Replicates are grouped together
6. I communicated this with the Coder/Designers so that they can design an appropriate expression table.