Week 9 - Revision history

Kdahlquist: /* Clustering and GO Term Enrichment with stem (part 2) */ delete section because moved to Week 10

2024-03-19T18:39:03Z

‎Clustering and GO Term Enrichment with stem (part 2): delete section because moved to Week 10

Kdahlquist: /* Homework Partners */ remove reference to group and replace with partners

2024-03-19T18:38:15Z

‎Homework Partners: remove reference to group and replace with partners

Kdahlquist: add interim deadline

2024-03-18T17:50:20Z

add interim deadline

Kdahlquist: /* Statistical Analysis Part 1: ANOVA */ add deadline

2024-03-18T17:49:27Z

‎Statistical Analysis Part 1: ANOVA: add deadline

Kdahlquist: /* Statistical Analysis Part 1: ANOVA */ stopping point for 3/14

2024-03-18T17:48:54Z

‎Statistical Analysis Part 1: ANOVA: stopping point for 3/14

Kdahlquist: /* Background */ change header to overview

2024-03-14T17:07:35Z

‎Background: change header to overview

Kdahlquist: /* Clustering and GO Term Enrichment with stem (part 2) */ remove reference to stopping point for week 8

2024-03-14T17:04:49Z

‎Clustering and GO Term Enrichment with stem (part 2): remove reference to stopping point for week 8

Kdahlquist: /* Calculate the Benjamini & Hochberg p value Correction */ comment out the interim deadline

2024-03-14T17:02:38Z

‎Calculate the Benjamini & Hochberg p value Correction: comment out the interim deadline

Kdahlquist: /* Statistical Analysis Part 1: ANOVA */ remove extraneous .

2024-03-14T17:00:44Z

‎Statistical Analysis Part 1: ANOVA: remove extraneous .

Kdahlquist: /* Statistical Analysis Part 1: ANOVA */ clarify what gets pasted to new sheet

2024-03-14T16:58:16Z

‎Statistical Analysis Part 1: ANOVA: clarify what gets pasted to new sheet

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 * Comparing results with known data:  the expression of the gene ''NSR1'' (ID: YGR159C)is known to be induced by cold shock. '''''Find ''NSR1'' in your 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?'''''  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?
 ==== Data and Files ====

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 === Homework Partners ===
-You will work in groups of three or four for the next two weeks of assignments.  You will keep the same group for the next two weeks. Please sit next to your group members in class.  You will be expected to consult with your group members, in order to complete the assignment.  However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).  Homework partners for this week are:
+You will keep the same partner for the next two weeks. Please sit next to your partner in class.  You will be expected to consult with your partner, in order to complete the assignment.  However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).  Homework partners for this week are:
 * Katie & Dean ([[Media:BIOL367_S24_microarray-data_wt.xlsx | wild type data]])

← Older revision		Revision as of 17:50, 18 March 2024
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	'''This journal entry is due on Thursday, March 21, at 12:01am Pacific time.'''		'''This journal entry is due on Thursday, March 21, at 12:01am Pacific time.'''
		+
		+	'''''Note that there is an interim deadline of Tuesday, March 19, 12:01am Pacific time to upload the spreadsheet you completed on Thursday and link to it on your individual journal page.'''''

	== Objectives ==		== Objectives ==

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 #* Be sure to undo any filters that you have applied before making any additional calculations.
-'''''Stopping point for Thursday, March 14.  Be sure to upload your spreadsheet to this wiki and link to it on your individual Week 9 journal page.'''''
+'''''Stopping point for Thursday, March 14.  Be sure to upload your spreadsheet to this wiki and link to it on your individual Week 9 journal page by Tuesday, March 19, 12:01am.'''''
 ==== Calculate the Bonferroni and p value Correction ====

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 #* Excel will now only display the rows that correspond to data meeting that filtering criterion.  A number will appear in the lower left hand corner of the window giving you the number of rows that meet that criterion.  We will check our results with each other to make sure that the computations were performed correctly.
 #* Be sure to undo any filters that you have applied before making any additional calculations.
 ==== Calculate the Bonferroni and p value Correction ====

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 We will be working on the protocols in class on Thursday, March 14 and Tuesday, March 19.  Based on the progress that is made during class, the milestone of what needs to be completed by the Week 9 journal deadline will be announced in class.  We will continue with this protocol for the Week 10 assignment.
-==== Background ====
+==== Overview ====
 This is a list of steps required to analyze DNA microarray data.

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 ## In section 4 (Execute) click on the yellow Execute button to run STEM.
 ##* If you get an error, there are some known reasons why stem might not work.  If you had #DIV/0! errors in your input file, it will cause problems. Re-open your file and open the Find/Replace dialog.  Search for #DIV/0!, but don't put anything in the replace field.  Click "Replace all" to remove the #DIV/0! errors.  Then save your file and try again with stem.
 # '''Viewing and Saving STEM Results'''
 ## A new window will open called "All STEM Profiles (1)".  Each box corresponds to a model expression profile.  Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value.  Profiles with the same color belong to the same cluster of profiles.  The number in each box is simply an ID number for the profile.

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 * '''''Zip and upload the .xlsx file that you have just created to the wiki.'''''
-'''''You must finish up to this point for the interim deadline of Tuesday, October 22, 12:01am Pacific time, so that the instructor can check your calculations before class.'''''
+<!--'''''You must finish up to this point for the interim deadline of Tuesday, March 19, 12:01am Pacific time, so that the instructor can check your calculations before class.'''''-->
 ==== Sanity Check: Number of genes significantly changed ====

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 #* Replace the phrase <(STRAIN)_SS_full> with the cell designation.
 #* Copy to the whole column.
-# In the first cell below the (STRAIN)_p-value header, type <code>=FDIST(<(STRAIN)_Fstat>,5,n-5)</code> replacing the phrase <(STRAIN)_Fstat> with the cell designation and the "n" as in (13) with the number of data points total. <!--(Again, note that the number of timepoints is actually "4" for the dSWI4 strain)-->.  Copy to the whole column.
+# In the first cell below the (STRAIN)_p-value header, type <code>=FDIST(<(STRAIN)_Fstat>,5,n-5)</code> replacing the phrase <(STRAIN)_Fstat> with the cell designation and the "n" as in (13) with the number of data points total. <!--(Again, note that the number of timepoints is actually "4" for the dSWI4 strain)--> Copy to the whole column.
 # Before we move on to the next step, we will perform a quick sanity check to see if we did all of these computations correctly.
 #*  Click on cell A1 and click on the Data tab.  Select the Filter icon (looks like a funnel). 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.

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 # Create a new worksheet, naming it "(STRAIN)_ANOVA" as appropriate.  For example, you might call yours "wt_ANOVA" or "dCIN5_ANOVA".
-# 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.
+# Copy all data from the "Master_Sheet" worksheet and paste it in your new worksheet.
-# At the top of the first column to the right of your data, create five column headers of the form (STRAIN)_AvgLogFC_(TIME) where STRAIN is your strain designation and (TIME) is 15, 30, etc.
+# At the top of the first column to the right of your data, create five column headers of the form (STRAIN)_AvgLogFC_(TIME) where STRAIN is your strain designation and (TIME) is 15, 30, 60, 90, and 120.
 # In the cell below the (STRAIN)_AvgLogFC_t15 header, type <code>=AVERAGE(</code>
 # Then highlight all the data in row 2 associated with t15, press the closing paren key (shift 0),and press the "enter" key.