Data Analysis - Revision history

Kdahlquist: /* Milestone 5: Clustering with stem and YEASTRACT */ instructions on how to use GO for enrichment

2019-11-26T23:28:40Z

‎Milestone 5: Clustering with stem and YEASTRACT: instructions on how to use GO for enrichment

Kdahlquist: /* Milestone 3: Getting the data ready for analysis */ add team names

2019-11-22T00:12:31Z

‎Milestone 3: Getting the data ready for analysis: add team names

Kdahlquist: /* Milestones */ add note about shared journal entries

2019-11-20T00:40:20Z

‎Milestones: add note about shared journal entries

Kdahlquist: /* Milestone 3: Getting the data ready for analysis */ add mention of QA's

2019-11-19T19:08:55Z

‎Milestone 3: Getting the data ready for analysis: add mention of QA's

Kdahlquist: /* Guild Members */ pasted in team names

2019-11-18T22:39:06Z

‎Guild Members: pasted in team names

Kdahlquist: /* Milestones */ added days/weeks

2019-11-18T22:37:49Z

‎Milestones: added days/weeks

Kdahlquist: /* Milestone 3: Complete Microarray Data Analysis */ separated out the milestones more granularly

2019-11-18T22:37:21Z

‎Milestone 3: Complete Microarray Data Analysis: separated out the milestones more granularly

Kdahlquist: /* Milestone 3: Complete Microarray Data Analysis */ add links to weekly journals

2019-11-18T22:34:41Z

‎Milestone 3: Complete Microarray Data Analysis: add links to weekly journals

Kdahlquist: /* Milestone 3: Complete Microarray Data Analysis */ note about column header

2019-11-18T22:30:49Z

‎Milestone 3: Complete Microarray Data Analysis: note about column header

Kdahlquist: /* Milestone 3: Complete Microarray Data Analysis */ start filling out steps

2019-11-18T22:30:09Z

‎Milestone 3: Complete Microarray Data Analysis: start filling out steps

@@ Line 45: / Line 45: @@
 # Cluster the data with stem, as you did on [[Week 9]].
-#* Note that we will make some adjustments to the GO term analysis because stem was not providing GO term names.
+#* Note that we will make some adjustments to the GO term analysis because stem was not providing GO term names.  We are going to use the GO enrichment tool at GeneOntology.org instead.
 # Use YEASTRACT to generate a candidate gene regulatory network as you did on [[Week 9]].

@@ Line 26: / Line 26: @@
 # Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.
-#* [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]
+#* [[Skinny Genes]]: [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]
-#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
+#* [[FunGals]]: [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
-#* [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]
+#* [[Sulfiknights]]: [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]
 # 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.
 #* Come up with consistent column headers that summarize this information

← Older revision		Revision as of 00:40, 20 November 2019
Line 12:		Line 12:

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

	=== Milestone 1: Annotated Bibliography ===		=== Milestone 1: Annotated Bibliography ===

@@ Line 27: / Line 27: @@
 #* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
 #* [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]
-# Make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
+# 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.
 #* 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.

@@ Line 5: / Line 5: @@
 == Guild Members ==
-* Ivy, Marcus
+* [[Sulfiknights]]: Ivy, Marcus
-* Emma, Kaitlyn
+* [[FunGals]]: Emma, Kaitlyn
-* Aby, David
+* [[Skinny Genes]]: Aby, David
 == Milestones ==

@@ Line 11: / Line 11: @@
 == Milestones ==
-The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together.
+The milestones do not necessarily correspond to particular days/weeks; instead they are sets of tasks grouped together.
 === Milestone 1: Annotated Bibliography ===

@@ Line 21: / Line 21: @@
 * The Data Analysts will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.
-=== Milestone 3: Complete Microarray Data Analysis ===
+=== Milestone 3: Getting the data ready for analysis ===
 # Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.
@@ Line 34: / Line 34: @@
 #* Data columns are to the right, in increasing chronological order, using the column header pattern you created
 #* Replicates are grouped together
 # Perform an ANOVA analysis of the data, as you did on [[Week 8]] for the Dahlquist lab data.
 #* Note that you will need to adjust your formulas to take into account the different number of timepoints and replicates in your article's dataset.
 # Cluster the data with stem, as you did on [[Week 9]].
 #* Note that we will make some adjustments to the GO term analysis because stem was not providing GO term names.
 # Use YEASTRACT to generate a candidate gene regulatory network as you did on [[Week 9]].
 # Create an input workbook for GRNmap based on a Microsoft Access database that the Coder/Designer and QA's make, following protocol in [[Week 10]]
 # Run GRNmap and interpret data.

@@ Line 32: / Line 32: @@
 # 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
+#* Data columns are to the right, in increasing chronological order, using the column header pattern you created
 #* Replicates are grouped together
 # Perform an ANOVA analysis of the data.

@@ Line 23: / Line 23: @@
 === Milestone 3: Complete Microarray Data Analysis ===
-* Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.
+# Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.
-** [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]
+#* [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]
-** [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
+#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
-** [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]
+#* [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]
-* Make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
+# Make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
-** 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.
-* Perform an ANOVA analysis of the data.
+# Organize the data in a worksheet in an Excel workbook so that:
-* Cluster the data with stem.
+#* ID is in the first column
-* Use YEASTRACT to generate a candidate gene regulatory network.
+#* Data columns are to the right, in increasing chronological order
-* Create an input workbook for GRNmap based on a Microsoft Access database that the Coder/Designer and QA's make.
+#* Replicates are grouped together
-* Run GRNmap and interpret data.
+# Perform an ANOVA analysis of the data.
-* As the end-user of the Access database, the Data Analysts will provide feedback to the QAs and Coder/Designer about the usability of database.
+# Cluster the data with stem.
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 [[Category:Group Projects]]