Difference between revisions of "Johnllopez Week 8"
(Explained how I did the Benjamini and Hochberg p value Correction.) |
(Change to my Statistical Analysis Part 1 values.) |
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Our total n would be 16 because we are analyzing 4 time points and we have 4 replicates. | Our total n would be 16 because we are analyzing 4 time points and we have 4 replicates. | ||
| − | After letting 16 = n, we applied the two following functions in order to receive our dSWI4_Fstat and dsWI4_p-values: =((n- | + | After letting 16 = n, we applied the two following functions in order to receive our dSWI4_Fstat and dsWI4_p-values: =((n-4)/4)*(Y2-AD2) and =FDIST(AE2,4,n-4). |
Next, I filtered through my p-value data to show only p-values less than 0.05. The result was 5475 records found. | Next, I filtered through my p-value data to show only p-values less than 0.05. The result was 5475 records found. | ||
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===Benjamini and Hochberg p value Correction=== | ===Benjamini and Hochberg p value Correction=== | ||
| − | To do this, I created a new worksheet to represent the Benjamini and Hochberg p value Correction calculations. I copied the "MasterIndex", "ID", and "Standard Names" columns from the master sheet and the "p-values" sheet from the ANOVA sheet. Then, I sorted these values from smallest to largest by p-value. This was necessary to achieve an index from smallest p-value to largest. Then, I applied the 2 Benjamini and Hochberg p-value correction formulas, which were (D2*6189)/E2 and =IF(F2>1,1,F2). Finally, I put the values in ascending order by MasterIndex. | + | To do this, I created a new worksheet to represent the Benjamini and Hochberg p value Correction calculations. I copied the "MasterIndex", "ID", and "Standard Names" columns from the master sheet and the "p-values" sheet from the ANOVA sheet. Then, I sorted these values from smallest to largest by p-value. This was necessary to achieve an index from smallest p-value to largest. Then, I applied the 2 Benjamini and Hochberg p-value correction formulas, which were (D2*6189)/E2 and =IF(F2>1,1,F2). Finally, I put the values in ascending order by MasterIndex, and copied the last column into my ANOVA file. |
| + | ===Sanity Check: Number of genes significantly changed=== | ||
==My Spreadsheet== | ==My Spreadsheet== | ||
[[File:JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | Here]]is my document. | [[File:JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | Here]]is my document. | ||
Revision as of 01:32, 24 October 2017
Contents
Electronic Lab Notebook
Experimental Design and Getting Ready
The strain comparison I used is dSWI_4, the dat individual dataset that you will analyze, the filename, the number of replicates for each strain and each time point in your data.
Classwork
The first steps I took to complete this assignment were performed in class as I followed along to Dr. Dahlquist's instructions. Note that each time the list below advances 1 number, I performed a save.
- After initially downloading the Excel document, I went through and deleted all of the columns that did not relate to me and my partner's strain (dsWI4). Then, I went through the data and replaced cells with "NA" with a blank string. There were 3641 replacements.
- I then created a new worksheet, naming it
Our total n would be 16 because we are analyzing 4 time points and we have 4 replicates.
After letting 16 = n, we applied the two following functions in order to receive our dSWI4_Fstat and dsWI4_p-values: =((n-4)/4)*(Y2-AD2) and =FDIST(AE2,4,n-4).
Next, I filtered through my p-value data to show only p-values less than 0.05. The result was 5475 records found.
Bonferonni and p value Correction
I started this section by creating two new colums with the label "dsWI4_Bonferonni_p-value". Next, I filled the entire first column of that using the following equation: (dSWI4_p-value * 6189) and filled the column AG. Letting that result = AG, I filled the column AE by using the following formula: =IF(AG2>1,1,AG2).
Benjamini and Hochberg p value Correction
To do this, I created a new worksheet to represent the Benjamini and Hochberg p value Correction calculations. I copied the "MasterIndex", "ID", and "Standard Names" columns from the master sheet and the "p-values" sheet from the ANOVA sheet. Then, I sorted these values from smallest to largest by p-value. This was necessary to achieve an index from smallest p-value to largest. Then, I applied the 2 Benjamini and Hochberg p-value correction formulas, which were (D2*6189)/E2 and =IF(F2>1,1,F2). Finally, I put the values in ascending order by MasterIndex, and copied the last column into my ANOVA file.
Sanity Check: Number of genes significantly changed
My Spreadsheet
File:JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zipis my document.
