Hivanson Week 13 - Revision history

Hivanson: /* We completed Milestone 2 */ are-->were

2024-04-18T06:23:56Z

‎We completed Milestone 2: are-->were

Hivanson: /* We completed Milestone 2 */ I fixed the tense of a sentence

2024-04-18T06:23:38Z

‎We completed Milestone 2: I fixed the tense of a sentence

Hivanson: really actually fixing classmate page links

2024-04-18T06:22:51Z

really actually fixing classmate page links

Hivanson: /* Acknowledgments */ fixed classmate links

2024-04-18T06:22:14Z

‎Acknowledgments: fixed classmate links

Hivanson: /* Acknowledgments */ signed acknowledgments

2024-04-18T06:21:59Z

‎Acknowledgments: signed acknowledgments

Hivanson: References

2024-04-18T06:20:04Z

References

Hivanson: template

2024-04-18T06:07:00Z

template

Hivanson: header

2024-04-18T05:58:17Z

header

Hivanson: all milestone 2 described

2024-04-18T05:57:59Z

all milestone 2 described

Hivanson: editing to fit what actually happened

2024-04-18T04:02:07Z

editing to fit what actually happened

@@ Line 13: / Line 13: @@
 #* 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
+#* Treatments were grouped together
-#* Replicates are grouped together
+#* Replicates were grouped together
 # I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

@@ Line 3: / Line 3: @@
 #*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.
 # 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.
-# Report on these quality measures:
+# I reported on the following 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.

@@ Line 18: / Line 18: @@
 ===Acknowledgments===
-I worked closely with [[Kmill104|Katie]] and [[Ckapla12|Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.
+I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.
 Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

@@ Line 18: / Line 18: @@
 ===Acknowledgments===
-I worked closely with [[Kmill104 Katie]] and [[Ckapla12 Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.
+I worked closely with [[Kmill104|Katie]] and [[Ckapla12|Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.
 Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

@@ Line 18: / Line 18: @@
 ===Acknowledgments===
-I worked closely with Katie and Charlotte, the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.
+I worked closely with [[Kmill104 Katie]] and [[Ckapla12 Charlotte]], the Data Analysts this week during class on 4/11/2024 and 4/16/2024, as well as at the LMU library on 4/17/2024 to complete Milestone 2 and begin Milestone 3.
 ===References===

@@ Line 16: / Line 16: @@
 #* Replicates are grouped together
 # I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.
 {{Hivanson}}
 {{Yeast_Beasts}}

← Older revision		Revision as of 06:07, 18 April 2024
Line 16:		Line 16:
	#* Replicates are grouped together		#* Replicates are grouped together
	# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.		# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.
		+
		+	{{Hivanson}}
		+	{{Yeast_Beasts}}

← Older revision		Revision as of 05:58, 18 April 2024
Line 1:		Line 1:
		+	===We completed Milestone 2===
	# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.		# 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.		#*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.

@@ Line 3: / Line 3: @@
 # 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.
 # Report on these quality measures:
-#* 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?
+#**As described above, the samples listed in the paper were all present in the dataset.
-# Come up with consistent column headers that summarize this information
+#* '''Are all the samples in the dataset described in the paper?'''
-#* For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.
+#**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.
-#* Do not use any special characters except for "-" or "_" (e.g., no commas, etc.)
+# We came up with consistent column headers that summarize this information
-# Organize the data in a worksheet in an Excel workbook so that:
+#* CHP_LogFC_timepoint-trial or Control_LogFC_timepoint-trial are used in our Excel analysis.
-#* ID (SGD systematic name) is in the first column
+# I ensured the data were organized in a worksheet in an Excel workbook so that:
-#* Data columns are to the right, in increasing chronological order, using the column header pattern you created
+#* ID (SGD systematic name) was in the first column
 #* Treatments are grouped together
 #* Replicates are grouped together
-# This information needs to be relayed to the Coder/Designers so that they can design an appropriate <code>expression</code> table.
+# I communicated this with the Coder/Designers so that they can design an appropriate <code>expression</code> table.

@@ Line 1: / Line 1: @@
-# Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.
+# I downloaded and examined the microarray dataset, and compared it to the samples and experiment described in your journal club article.
-#* [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip Link to processed dataset from SGD.]
+#*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.
-#* 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.
+# 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.
 # Report on these quality measures:
 #* Are all the samples described in the paper in the dataset?