Difference between revisions of "Emilysimso Week 8"
From LMU BioDB 2015
Emilysimso (Talk | contribs) (Formatting) |
Emilysimso (Talk | contribs) (Some changes, updates, questions) |
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==Part One== | ==Part One== | ||
| − | + | Opened up the spreadsheet for the first time | |
| − | + | * Taken from [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Minds Part 1] | |
| − | + | Scaled and centered the data | |
| − | + | * It was important to always reference back to the same rows using a dollar sign symbol attached to B2 and B3 (becoming B2$ and B2$) because we want to always compare the other call to these numerical values. | |
| − | + | Performed statistical analysis on the data (averages, StdDev, Tstat, Pvalue, Bonferroni Pvalue) | |
| − | + | File after work day on October 15, 2015 - [[File:Copy of Merrell Compiled Raw Data Vibrio ES 20151015.xls]] | |
| + | Updated Files | ||
* Xcel file after work day on October 20, 2015 - [[File:Copy of Merrell Compiled Raw Data Vibrio ES 20151020.xls]] | * Xcel file after work day on October 20, 2015 - [[File:Copy of Merrell Compiled Raw Data Vibrio ES 20151020.xls]] | ||
* .txt. file after work day on October 20, 2015 - [[File:Copy of Merrell Compiled Raw Data Vibrio ES 20151020.txt]] | * .txt. file after work day on October 20, 2015 - [[File:Copy of Merrell Compiled Raw Data Vibrio ES 20151020.txt]] | ||
| + | ===Questions=== | ||
* 99 genes have a P value < 0.05 | * 99 genes have a P value < 0.05 | ||
* 19 genes have a P value < 0.01 | * 19 genes have a P value < 0.01 | ||
* 1 gene has a P value < 0.001 | * 1 gene has a P value < 0.001 | ||
* No genes have a P value < 0.0001 | * No genes have a P value < 0.0001 | ||
| − | * These values do not match with known values given in instructions from Part 1 | + | ** These values do not match with known values given in instructions from Part 1 |
| + | |||
| + | Created a new spreadsheet | ||
| + | * [[File:Copy of Merrell Compiled Raw Data Vibrio ES 20151021.xlsx]] | ||
| + | * [[File:Copy of Merrell Compiled Raw Data Vibrio ES 20151021.txt]] | ||
| + | |||
| + | Responses to Questions | ||
| + | * 361 genes have a P value < 0.05 | ||
| + | * 94 genes have a P value < 0.01 | ||
| + | * 12 genes have a P value < 0.001 | ||
| + | * 1 gene has a P value < 0.0001 | ||
| + | * No genes have a Bonferroni-corrected P value < 0.05 - 0% | ||
| + | * No genes have a B-H corrected P value < 0.05 - 0% | ||
| + | * 149 genes have a Pvalue <0.05 and a Avg_LogFC_all > 0 | ||
| + | * 212 genes have a Pvalue <0.05 and a Avg_LogFC_all < 0 | ||
| + | * No genes have a Pvalue <0.05 and a Avg_LogFC_all >.25 and <0.05 | ||
| + | * 6 genes have a Pvalue <0.05 and a Avg_LogFC_all >.25 and <0.05 | ||
| + | |||
==Part Two== | ==Part Two== | ||
Revision as of 23:57, 20 October 2015
Part One
Opened up the spreadsheet for the first time
- Taken from Sample Minds Part 1
Scaled and centered the data
- It was important to always reference back to the same rows using a dollar sign symbol attached to B2 and B3 (becoming B2$ and B2$) because we want to always compare the other call to these numerical values.
Performed statistical analysis on the data (averages, StdDev, Tstat, Pvalue, Bonferroni Pvalue)
File after work day on October 15, 2015 - File:Copy of Merrell Compiled Raw Data Vibrio ES 20151015.xls
Updated Files
- Xcel file after work day on October 20, 2015 - File:Copy of Merrell Compiled Raw Data Vibrio ES 20151020.xls
- .txt. file after work day on October 20, 2015 - File:Copy of Merrell Compiled Raw Data Vibrio ES 20151020.txt
Questions
- 99 genes have a P value < 0.05
- 19 genes have a P value < 0.01
- 1 gene has a P value < 0.001
- No genes have a P value < 0.0001
- These values do not match with known values given in instructions from Part 1
Created a new spreadsheet
- File:Copy of Merrell Compiled Raw Data Vibrio ES 20151021.xlsx
- File:Copy of Merrell Compiled Raw Data Vibrio ES 20151021.txt
Responses to Questions
- 361 genes have a P value < 0.05
- 94 genes have a P value < 0.01
- 12 genes have a P value < 0.001
- 1 gene has a P value < 0.0001
- No genes have a Bonferroni-corrected P value < 0.05 - 0%
- No genes have a B-H corrected P value < 0.05 - 0%
- 149 genes have a Pvalue <0.05 and a Avg_LogFC_all > 0
- 212 genes have a Pvalue <0.05 and a Avg_LogFC_all < 0
- No genes have a Pvalue <0.05 and a Avg_LogFC_all >.25 and <0.05
- 6 genes have a Pvalue <0.05 and a Avg_LogFC_all >.25 and <0.05
Part Two
- Used the 2009 database
- There were 772 errors in this data
- Here is the file EX.txt - File:Copy of Merrell Compiled Raw Data Vibrio ES 20151020.EX.txt
