Hhinsch Week 8 - Revision history

Hhinsch: updated my power point slides so it aligns with week 8 and week 10

2017-11-07T07:02:25Z

updated my power point slides so it aligns with week 8 and week 10

Hhinsch: missed some corrections because I accidentally made them on the week 8 assignment page

2017-10-24T07:06:16Z

missed some corrections because I accidentally made them on the week 8 assignment page

Hhinsch: missed some corrections because I accidentally made them on the week 8 assignment page

2017-10-24T07:05:37Z

missed some corrections because I accidentally made them on the week 8 assignment page

Hhinsch: cvhanged strains

2017-10-24T06:59:57Z

cvhanged strains

Hhinsch: fixed more strains to dhmo1

2017-10-24T06:58:47Z

fixed more strains to dhmo1

Hhinsch: added another note to my favorite gene section

2017-10-24T06:03:06Z

added another note to my favorite gene section

Hhinsch: added a short electronic notebook section and wrote my summary paragraph

2017-10-24T06:00:31Z

added a short electronic notebook section and wrote my summary paragraph

Hhinsch: deleted one of my old excel zips from the page

2017-10-24T05:53:55Z

deleted one of my old excel zips from the page

Hhinsch: added week 8 to my references

2017-10-24T05:52:46Z

added week 8 to my references

Hhinsch: added my acknowledgments and my electronic signature

2017-10-24T05:49:36Z

added my acknowledgments and my electronic signature

@@ Line 105: / Line 105: @@
 ***As you can see, the gene expression changed due to the cold shock. It should be noted that the gene expression changed only slightly, wavering just above and below zero.
 * We will compare the numbers we get between the wild type strain and the other strains studied, organized as a table.  Use this [[Media:BIOL367_F17_sample_p-value_slide.pptx | sample PowerPoint slide]] to see how your table should be formatted. Upload your slide to the wiki.
-**[[Media:BIOL367_F17_dHMO1_p-value_slide_HH.pptx | dHMO1 PowerPoint slide]]
+**[[Media:BIOL367_F17_dHMO1_slides_HH.zip|BIOL367_F17_dHMO1_slides_HH.zip]]
 ==== Summary Paragraph ====

@@ Line 64: / Line 64: @@
 Before we move on to further analysis of the data, we want to perform a more extensive sanity check to make sure that we performed our data analysis correctly.  We are going to find out the number of genes that are significantly changed at various p value cut-offs.
-* Go to your (STRAIN)_ANOVA worksheet.
+* Go to your dHMO1_ANOVA worksheet.
 * Select row 1 (the row with your column headers) and select the menu item Data > Filter > Autofilter (The funnel icon on the Data tab).  Little drop-down arrows should appear at the top of each column.  This will enable us to filter the data according to criteria we set.
 * Click on the drop-down arrow for the unadjusted p value.  Set a criterion that will filter your data so that the p value has to be less than 0.05.

@@ Line 41: / Line 41: @@
 # Now we will perform adjustments to the p value to correct for the [https://xkcd.com/882/ multiple testing problem].  Label the next two columns to the right with the same label, dHMO1_Bonferroni_p-value.
-# Type the equation <code>=<(STRAIN)_p-value>*6189</code>, Upon completion of this single computation, use the Step (10) trick to copy the formula throughout the column.
+# Type the equation <code>=<dHMO1_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 (STRAIN)_Bonferroni_p-value header: <code>=IF(dHMO1_Bonferroni_p-value>1,1,dHMO1_Bonferroni_p-value)</code>, where "dHMO1_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.
+# 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 dHMO1_Bonferroni_p-value header: <code>=IF(dHMO1_Bonferroni_p-value>1,1,dHMO1_Bonferroni_p-value)</code>, where "dHMO1_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 52: / Line 52: @@
 # Type the header "Rank" in cell E1.  We will create a series of numbers in ascending order from 1 to 6189 in this column.  This is the p value rank, smallest to largest.  Type "1" into cell E2 and "2" into cell E3. Select both cells E2 and E3. Double-click on the plus sign on the lower right-hand corner of your selection to fill the column with a series of numbers from 1 to 6189.
 # Now you can calculate the Benjamini and Hochberg p value correction. Type dHMO1_B-H_p-value in cell F1. Type the following formula in cell F2: <code>=(D2*6189)/E2</code> and press enter. Copy that equation to the entire column.
-# Type "STRAIN_B-H_p-value" into cell G1.
+# Type "dHMO1_B-H_p-value" into cell G1.
 # Type the following formula into cell G2: <code>=IF(F2>1,1,F2)</code> and press enter. Copy that equation to the entire column.
 # Select columns A through G.  Now sort them by your MasterIndex in Column A in ascending order.

@@ Line 23: / Line 23: @@
 #* Upon completion of this single computation, use the Step (7) trick to copy the formula throughout the column.
 # Repeat this computation for the t30 through t120 data points.  Again, be sure to get the data for each time point, type the right number of data points, and get the average from the appropriate cell for each time point, and copy the formula to the whole column for each computation.
-# In the first column to the right of dHMO1_ss_t120, create the column header (STRAIN)_SS_full.
+# In the first column to the right of dHMO1_ss_t120, create the column header dHMO1_SS_full.
 # In the first row below this header, type <code>=sum(<range of cells containing "ss" for each timepoint>)</code> and hit enter.
 # In the next two columns to the right, create the headers dHMO1_Fstat and dHMO1_p-value.
@@ Line 40: / Line 40: @@
 ==== Calculate the Bonferroni and p value Correction ====
-# Now we will perform adjustments to the p value to correct for the [https://xkcd.com/882/ multiple testing problem].  Label the next two columns to the right with the same label, (STRAIN)_Bonferroni_p-value.
+# Now we will perform adjustments to the p value to correct for the [https://xkcd.com/882/ multiple testing problem].  Label the next two columns to the right with the same label, dHMO1_Bonferroni_p-value.
 # Type the equation <code>=<(STRAIN)_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 (STRAIN)_Bonferroni_p-value header: <code>=IF(STRAIN_Bonferroni_p-value>1,1,STRAIN_Bonferroni_p-value)</code>, where "STRAIN_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.
+# 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 (STRAIN)_Bonferroni_p-value header: <code>=IF(dHMO1_Bonferroni_p-value>1,1,dHMO1_Bonferroni_p-value)</code>, where "dHMO1_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 ====
-# Insert a new worksheet named "(STRAIN)_ANOVA_B-H".
+# Insert a new worksheet named "dHMO1_ANOVA_B-H".
 # Copy and paste the "MasterIndex", "ID", and "Standard Name" columns from your previous worksheet into the first two columns of the new worksheet.
 # For the following, use Paste special > Paste values.  Copy your unadjusted p values from your ANOVA worksheet and paste it into Column D.
 # Select all of columns A, B, C, and D. Sort by ascending values on Column D. Click the sort button from A to Z on the toolbar, in the window that appears, sort by column D, smallest to largest.
 # Type the header "Rank" in cell E1.  We will create a series of numbers in ascending order from 1 to 6189 in this column.  This is the p value rank, smallest to largest.  Type "1" into cell E2 and "2" into cell E3. Select both cells E2 and E3. Double-click on the plus sign on the lower right-hand corner of your selection to fill the column with a series of numbers from 1 to 6189.
-# Now you can calculate the Benjamini and Hochberg p value correction. Type (STRAIN)_B-H_p-value in cell F1. Type the following formula in cell F2: <code>=(D2*6189)/E2</code> and press enter. Copy that equation to the entire column.
+# Now you can calculate the Benjamini and Hochberg p value correction. Type dHMO1_B-H_p-value in cell F1. Type the following formula in cell F2: <code>=(D2*6189)/E2</code> and press enter. Copy that equation to the entire column.
 # Type "STRAIN_B-H_p-value" into cell G1.
 # Type the following formula into cell G2: <code>=IF(F2>1,1,F2)</code> and press enter. Copy that equation to the entire column.

@@ Line 103: / Line 103: @@
 ***90 = 0.022259535
 ***120 = -0.042916782
 * We will compare the numbers we get between the wild type strain and the other strains studied, organized as a table.  Use this [[Media:BIOL367_F17_sample_p-value_slide.pptx | sample PowerPoint slide]] to see how your table should be formatted. Upload your slide to the wiki.
 **[[Media:BIOL367_F17_dHMO1_p-value_slide_HH.pptx | dHMO1 PowerPoint slide]]

@@ Line 108: / Line 108: @@
 ==== Summary Paragraph ====
-* Write a summary paragraph that gives the conclusions from this week's analysis.
+* In summary, we learned how to utilize excel calculations in order to analyze the data. We found that as we performed different p-value calculations, the amount of the genes with a significant p-value changed. In regards to the p-value corrections, we found that not many of the genes changed expression as induced by the cold shock.
 ===Acknowledgments===

← Older revision		Revision as of 05:53, 24 October 2017
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	* Write a summary paragraph that gives the conclusions from this week's analysis.		* Write a summary paragraph that gives the conclusions from this week's analysis.
−	~~===excel files===~~
−	~~[[Media:Hhinsch_Week_8.zip]]~~

	===Acknowledgments===		===Acknowledgments===

← Older revision		Revision as of 05:52, 24 October 2017
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	===References===		===References===
		+
		+	#LMU BioDB 2017. (2017). Week 8. Retrieved October 19, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
		+
	{{hhinsch}}		{{hhinsch}}

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 ===Acknowledgments===
 ===References===
 {{hhinsch}}