Jnimmers Week 8 - Revision history

Jnimmers: formatting

2019-10-24T04:17:52Z

formatting

2019-10-24T03:42:18Z

format

2019-10-24T03:41:09Z

Invoke template

2019-10-24T03:40:09Z

Format

2019-10-24T03:34:28Z

Conclusion

2019-10-24T03:28:14Z

Methods and results

2019-10-24T03:27:23Z

Purpose

2019-10-24T03:24:51Z

method change

2019-10-24T03:23:39Z

Update methodology

2019-10-24T03:18:24Z

Update methods

@@ Line 119: / Line 119: @@
 #** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
 #*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu.  Undo the filter.  This ensures that we will cluster only the genes with a "significant" change in expression and not the noise.
-#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
+#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, dGLN_AvgLogFC_t15, etc.).
 #** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
 #** Save your work.  Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt).  Click OK to the warnings and close your file.

@@ Line 156: / Line 156: @@
 *"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 20:13, 23 October 2019 (PDT)
 ==References==
-Dahlquist, K. (2019, October 17). Week 8 [Wikipedia Page Post]. Retrieved from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8.
+*Dahlquist, K. (2019, October 17). Week 8 [Wikipedia Page Post]. Retrieved from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8.

← Older revision		Revision as of 03:41, 24 October 2019
Line 1:		Line 1:
		+	{{Jnimmers}}
	==Purpose==		==Purpose==
	The purpose of this assignment is to understand and utilize the STEM application and become more adept in utilizing and filtering data from a database/Excel formatted sheet.		The purpose of this assignment is to understand and utilize the STEM application and become more adept in utilizing and filtering data from a database/Excel formatted sheet.

@@ Line 46: / Line 46: @@
 # Type the equation <code>=<dGLN3_p-value>*6189</code>, Upon completion of this single computation, use the Step (10) trick to copy the formula throughout the column.
 # Replace any corrected p value that is greater than 1 by the number 1 by typing the following formula into the first cell below the second dGLN3_Bonferroni_p-value header: <code>=IF(dGLN3_Bonferroni_p-value>1,1, dGLN3_Bonferroni_p-value)</code>, where "dGLN3_Bonferroni_p-value" refers to the cell in which the first Bonferroni p value computation was made.  Use the Step (10) trick to copy the formula throughout the column.
 ==== Calculate the Benjamini & Hochberg p value Correction ====

@@ Line 142: / Line 142: @@
 ##* '''''This is the stopping point for the Week 8 assignment.'''''
 ==Data and Files==
 *[[Media: BIOL367_F19_microarray-data_dGLN3_JNM_1021.xlsx | Microarray Data Analysis Spreadsheet]]

@@ Line 1: / Line 1: @@
 ==Purpose==
 The purpose of this assignment is to understand and utilize the STEM application and become more adept in utilizing and filtering data from a database/Excel formatted sheet.
 ==== Statistical Analysis Part 1: ANOVA ====

← Older revision		Revision as of 03:27, 24 October 2019
Line 1:		Line 1:
		+	==Purpose==
		+	The purpose of this assignment is to understand and utilize the STEM application and become more adept in utilizing and filtering data from a database/Excel formatted sheet.
	==== Statistical Analysis Part 1: ANOVA ====		==== Statistical Analysis Part 1: ANOVA ====

@@ Line 3: / Line 3: @@
 The purpose of the within-stain ANOVA test is to determine if any genes had a gene expression change that was significantly different than zero at '''''any''''' timepoint.
-# Create a new worksheet, naming it either "dGLN3_ANOVA" as appropriate.  For example, you might call yours "wt_ANOVA" or "dHAP4_ANOVA"
+# Create a new worksheet, naming it either "dGLN3_ANOVA" as appropriate.
 # Copy the first three columns containing the "MasterIndex", "ID", and "Standard Name" from the "Master_Sheet" worksheet for your strain and paste it into your new worksheet.  Copy the columns containing the data for your strain and paste it into your new worksheet.
 # At the top of the first column to the right of your data, create five column headers of the form dGLN3_AvgLogFC_(TIME) where STRAIN is your strain designation and (TIME) is 15, 30, etc.

@@ Line 97: / Line 97: @@
 ***Yes, NSR1 changes expression due to cold shock
 Note that the average Log fold change is what we called "STRAIN)_AvgLogFC_(TIME)" in step 3 of the ANOVA analysis. Does ''NSR1'' change expression due to cold shock in this experiment?
-* For fun, find "your favorite gene" (from your [[Week 3]] assignment) in the dataset.  '''''What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values?  What is its average Log fold change at each of the timepoints in the experiment?'''''  Does your favorite gene change expression due to cold shock in this experiment?
+* For fun, find CMR2 "My favorite gene" in the dataset.  '''''What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values?  What is its average Log fold change at each of the timepoints in the experiment?'''''  Does your favorite gene change expression due to cold shock in this experiment?
 ***Bonferroni-corrected: 4753.794267
 ***B-H-corrected: 0.859326513