Quality Assurance - Revision history

Kdahlquist: /* Milestone 4: Validation, Quality Assurance, and Documentation of the Database */ paste in instructions for querying the access db

2024-04-26T16:52:37Z

‎Milestone 4: Validation, Quality Assurance, and Documentation of the Database: paste in instructions for querying the access db

Kdahlquist: remove under construction link

2024-04-11T04:59:00Z

remove under construction link

Kdahlquist: /* Milestone 6: Final Documentation */ delete because covered in previous milestone

2024-04-11T04:58:42Z

‎Milestone 6: Final Documentation: delete because covered in previous milestone

Kdahlquist: /* Milestone 4: Validation, Quality Assurance, and Documentation of the Database */ add feedback from data analysis

2024-04-11T04:58:24Z

‎Milestone 4: Validation, Quality Assurance, and Documentation of the Database: add feedback from data analysis

Kdahlquist: /* Milestone 5: Validation and Quality Assurance on Database */ paste in from coder

2024-04-11T04:57:22Z

‎Milestone 5: Validation and Quality Assurance on Database: paste in from coder

Kdahlquist: /* Milestone 4: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources */ paste in from coder/designer guild

2024-04-11T04:56:42Z

‎Milestone 4: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources: paste in from coder/designer guild

Kdahlquist: /* Milestone 4: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources */ save interim

2024-04-11T04:55:41Z

‎Milestone 4: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources: save interim

Kdahlquist: /* Milestone 3: Making sure expression data has both Sytematic Name and Standard Name ID's */ comment out R package

2024-04-11T04:52:03Z

‎Milestone 3: Making sure expression data has both Sytematic Name and Standard Name ID's: comment out R package

Kdahlquist: /* Milestone 2: Working with Data Analysts to understand microarray dataset */ adjust based on data analysist instructions

2024-04-11T04:50:59Z

‎Milestone 2: Working with Data Analysts to understand microarray dataset: adjust based on data analysist instructions

Kdahlquist: /* Milestone 2: Working with Data Analysts to understand microarray dataset */ change plural

2024-04-11T04:47:04Z

‎Milestone 2: Working with Data Analysts to understand microarray dataset: change plural

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 * QA's will collect feedback from the Data Analysts and communicate to the Coder/Designers any changes needed to the database.
 * With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
 {{Final Project Links}}
 [[Category:Team Project]]

← Older revision		Revision as of 04:59, 11 April 2024
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−	~~{{Under Construction}}~~
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	{{Final Project Links}}		{{Final Project Links}}

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 * QA's will collect feedback from the Data Analysts and communicate to the Coder/Designers any changes needed to the database.
 * With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
 {{Final Project Links}}
 [[Category:Team Project]]

@@ Line 70: / Line 70: @@
 ** In particular, the QA's need to make sure that all of the rows of data were imported into the database for each table.
 ** The QA's will make sure that both the ID (SGD systematic name) and Standard Names are included in the expression table and are correct.
-* QA's will communicate to the Coder/Designers any changes needed to the database.
+* QA's will collect feedback from the Data Analysts and communicate to the Coder/Designers any changes needed to the database.
 * With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]

@@ Line 65: / Line 65: @@
 *** 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 5: Validation and Quality Assurance on Database ===
+=== Milestone 4: Validation, Quality Assurance, and Documentation of the 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.
+* 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).
+** In particular, the QA's need to make sure that all of the rows of data were imported into the database for each table.
-** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.
+** The QA's will make sure that both the ID (SGD systematic name) and Standard Names are included in the expression table and are correct.
 * QA's will communicate to the Coder/Designers any changes needed to the database.
 === Milestone 6: Final Documentation ===

@@ Line 50: / Line 50: @@
 <!--* Here is a [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package] for it, too.-->
-=== Milestone 4: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources ===
+=== Milestone 3: Design a database to store data needed to create a GRNmap input workbook ===
 ** Databases created by the teams will be kept in a [https://lmu.box.com/s/lorqp5d5hkzqb7q161ldb66mhqfham3f "BIOL367_Spring2024" 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.
 === Milestone 5: Validation and Quality Assurance on Database ===

@@ Line 51: / Line 51: @@
 === Milestone 4: 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 [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].
@@ Line 63: / Line 65: @@
 ** 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 5: Validation and Quality Assurance on Database ===

@@ Line 25: / Line 25: @@
 As an overview, the QA team members are 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 Analysts. The QA's 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 Analysts, 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:
+# Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.
-* Along with the Data Analysts, download the microarray data associated with your group's article.
+#* [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip Link to processed dataset from SGD.]
-** [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]
+#* For your reference, this is the link to the dataset at the GEO Database:[https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GSE26169].  However, we will use the dataset processed by SGD.
-** [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
+# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
-** [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]
+# Report on these quality measures:
-** 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 described in the paper in the dataset?
+#* Are all the samples in the dataset described in the paper?
-** Are all the samples in the dataset described in the paper?
+# Come up with consistent column headers that summarize this information
-* 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.
-** 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.)
-* Organize the data in a worksheet in an Excel workbook so that:
+# Organize the data in a worksheet in an Excel workbook so that:
-* ID is in the first column
+#* 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
+#* Data columns are to the right, in increasing chronological order, using the column header pattern you created
-* Replicates are grouped together
+#* Treatments are grouped together
 === Milestone 3:  Making sure expression data has both Sytematic Name and Standard Name ID's ===

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 === Milestone 2: 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.
+As an overview, the QA team members are 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 Analysts. The QA's 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 Analysts, 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: