Quality Assurance

Final Project Links
Overview	Deliverables	Guilds	Project Manager	Quality Assurance	Data Analysis	Coder/Designer
		Teams	FunGals	Sulfiknights	Skinny Genes

The QA team member is the link between the Coder/Designer and the Data Analyst. He or she needs to know the details of the microarray dataset being analyzed so that the database being designed and populated by the Coder/Designer is correct and useful for the Data Analyst. The QA also makes sure that the data analysis steps are being performed correctly and are being correctly documented.

Guild Members

• FunGals: Iliana
• Skinny Genes: Jonar, Christina
• Sulfiknights: Naomi, Joey

Milestones

The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together.

• Data Analysts and QA's who have a partner in their group can have a shared individual journal entry. Both students will be given the same grade and are expected to contribute equally to the electronic lab notebook.
• Detailed notes should be taken throughout consistent with reproducible research and contributing to the final deliverables.

Milestone 1: Annotated Bibliography

• The QA's will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.

Milestone 2: Journal Club Presentation

• The QA's will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.

Milestone 3: Working with Data Analysts to understand microarray dataset

As an overview, the QA team member is the link between the Coder/Designer and the Data Analyst. He or she needs to know the details of the microarray dataset being analyzed so that the database being designed and populated by the Coder/Designer is correct and useful for the Data Analyst. The QA will independently check that all of the data retrieved from SGD is present and accurately represented in the MS Access database. The QA will also provide assistance to the Data Analyst, making sure that the data analysis steps are being performed correctly and are being correctly documented.

Initially, the QA's will need to do the following:

• Along with the Data Analysts, download the microarray data associated with your group's article.
  • Barreto et al. (2012)
  • Kitagawa et al. (2002)
  • Thorsen et al. (2007)
  • Along with the Data Analysts, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
  • Are all the samples described in the paper in the dataset?
  • Are all the samples in the dataset described in the paper?
• 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.
• Organize the data in a worksheet in an Excel workbook so that:
• ID is in the first column
• Data columns are to the right, in increasing chronological order, using the column header pattern you created
• Replicates are grouped together

Milestone 4: Making sure expression data has both Sytematic Name and Standard Name ID's

• The design of the expression tables in the final database will need both an ID field (yeast systematic name) and Standard Name fields.
• You will need to check the IDs in the expression data and potentially populate one or both of these fields.
• One way to do this is use the "ORF List <-> Gene List" tool at YEASTRACT.
• The Synergizer website may also be helpful.
• Here is a Bioconductor package for it, too.

Milestone 5: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources

• Databases created by the teams will be kept in a "BIOL367_Fall2019 > Final Project Database" Box folder.
• Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.
• This folder will serve as as the version control mechanism for the Coder/Designer guild.
• Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.
• The starting point will be the database already used for the Week 10 assignment, which can be found here on Box.
  • This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.
    • You may need to change the table names of these existing tables so that they make sense with the overall database design.
  • You will need to add one or more expression tables for the expression data from your team's article.
    • Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.
  • You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.
    • A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.

Milestone 6: Validation and Quality Assurance on Database

• After the Access database is built by the Coder/Designer, the QA will perform quality assurance to make sure that the database is correct and accurate.
  • In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).
  • The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.
• QA's will communicate to the Coder/Designers any changes needed to the database.

Milestone 7: Final Documentation

• With the Coder/Designer, finalize the database schema diagram

Final Project Links
Overview	Deliverables	Guilds	Project Manager	Quality Assurance	Data Analysis	Coder/Designer
		Teams	FunGals	Sulfiknights	Skinny Genes