Emilysimso Week 14
From LMU BioDB 2015
Contents
Goal
- GenMAPP Users should complete the statistical analysis of the microarray data, import the data into GenMAPP, and run MAPPFinder.
Initial Procedure
- Created a new CompiledRawData spreadsheet
- Column 1 = ID
- Column 2 = MasterIndex (has numbers 1-10819)
- Sheet 1 was labeled Compiled Raw Data
- Took the log data from the 1, 5, 20, and 60 time points - had 16 total data columns (four for each time point)
- Created MasterSheet in sheet 2
- Deleted 704 rows after alphabetizing data A-Z according to the ID number because they were controls (started with Blank, blank, gDNA, NC-, or ORF)
- 1333 cells have the error #NUM!
- Replaced these with nothing so that the cells are blank
- Created ScalingCentering in sheet 3
- Copied over data from MasterSheet
- Added two extra rows on top of data for Average and Standard Deviation
- Some of the columns had divided by zero errors for the average and standard deviation
- Had to delete #DIV/0! that came up for some of the genes in these columns
- Made the cells that contained this error blank by searching for "DIV" and using the replace function to make this blank
- C1_rep2 - 2 replacements
- C5_rep4 - 1 replacement
- C20_rep2 - 2 replacements
- C20_rep3 - 1 replacement
- C20_rep4 - 1 replacement
- C60_rep1 - 2 replacements
- C60_rep2 - 1 replacement
- For the scaled and centered columns in the ScalingCentering tab - used the equation =(C4-C$2)/C$3 (for the first column)
- Had to run the data through a script to get rid of duplicates
- Calculated the averages for the technical replicates for each of the time points
- Created a new tab labeled Statistics
- Copied the technical averages into this tab
- Calculated the biological averages for each time point
- Calculated the Average Log Ratios by subtracting the value for C0 from each of the C points and subtracting C60 from each of the F points
- To calculate the pvalues - had to compare the C values to C1 and the F values to C60
- Used TTEST(array 1, array 2, 2, 3)
- Created new Sheet - Bonferroni_Pvalue
- Calculated the Bonferroni Pvalues for each of the comparisons
- Created new Sheet - B-H_Pvalue
- Calculated the Benjamin and Hochberg Pvalue for each of the comparisons
- Created new Sheet - forGenMAPP
- Copied columns A-AP from statistics worksheet
Edits to Match with Ron
- Took Compiled_Raw_Data from Ron's spreadsheet
- Created a Master_Sheet
- Deleted 3011 #NUM! error cells
- Deleted 704 rows the started incorrectly
- Created Scaling_Centering sheet
- Replaced 32 cells with #DIV/0! to read 'error'
- Uploaded new updated file (see below)
- Received split data from Dr. Dahlquist
- Averaged the two split data points for each replicate at each time point (4 each for C0, C5, etc.)
- Copied these averages to a new sheet labeled Statistics
- Averaged the biological replicates for each time point
- Calculated the average log ratio for C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60
- Calculated the ttest for the above relationships
Files
- File:CompiledRawData 20151201 HMH.xlsx
- File:UpdatedCompiledRawData 20151206 HMH.xlsx
- File:ForGenMAPP 20151203 HMH.xlsx
- File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx
Weekly Assignment Information
Assignments
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 13
- Week 14
- Week 15
Individual Journal Entries
- Emilysimso Week 2
- Emilysimso Week 3
- Emilysimso Week 4
- Emilysimso Week 5
- Emilysimso Week 6
- Emilysimso Week 7
- Emilysimso Week 8
- Emilysimso Week 9
- Emilysimso Week 10
- Emilysimso Week 11
- Emilysimso Week 12
- Emilysimso Week 13
- Emilysimso Week 14
- Emilysimso Week 15
Class Journal Entries
- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 4
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 7
- Class Journal Week 8
- Class Journal Week 9
- Class Journal Week 10
- Class Journal Week 11
- Class Journal Week 12
- Class Journal Week 13
- Class Journal Week 14
- Class Journal Week 15
