Difference between revisions of "Taur.vil Week 8"
From LMU BioDB 2013
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==Digital Notebook:== | ==Digital Notebook:== | ||
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| + | ===Th 10/10/2013=== | ||
# Downloaded original data (Merrell_Compiled_Raw_Data_Vibrio.xls) from [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae]] | # Downloaded original data (Merrell_Compiled_Raw_Data_Vibrio.xls) from [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae]] | ||
# Observed that the data collected had already been log transformed (there were negative numbers) | # Observed that the data collected had already been log transformed (there were negative numbers) | ||
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# Copied into a new page titled forGenMAPP and inserted column 2 (System Code) where N was entered for each row. | # Copied into a new page titled forGenMAPP and inserted column 2 (System Code) where N was entered for each row. | ||
| + | ===Tu 10/15/2013=== | ||
| + | #Downloaded GenMAPP, my text files, and the 2009 Vibrio cholerae Gene Database | ||
| + | #Set the database to the downloaded 2009 Vibrio cholerae Gene Database | ||
| + | #In Expression Dataset Manager, created a new dataset by importing my txt for GenMAPP File | ||
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| + | 772 errors while creating a new dataset; errors in dataset or just could not find IDs | ||
| + | : in the exception file reported that the gene was not found, confirmed this was the case for all 772 errors by filtering | ||
Revision as of 17:05, 15 October 2013
Uploaded Files:
Contents |
Part One Document Files:
Digital Notebook:
Th 10/10/2013
- Downloaded original data (Merrell_Compiled_Raw_Data_Vibrio.xls) from [[1]]
- Observed that the data collected had already been log transformed (there were negative numbers)
- Meant we could begin at the normalization step
- Created a new sheet in Excell, titled scaled_centered.
- In scaled_centered, inserted two new rows and calculated average and standard deviation for each replicate using the excell functions AVERAGE and STDEV.
- Created a new column for each of the samples, relabeling them with a _sc (for scaled centered) after the name. Filled these columns with the scaled centered values calculated by taking the raw data minus the average for the sample (row 2) divided by the standard deviation (row 3).
- created a new worksheet called statistics and copied the ID column into the new worksheet.
- Pasted values only for the scaled and centered columns.
- Deleted the rows for average and standard deviation
- Inserted columns to the right of the data for the average log fold change (FC) of patient and calculated the value by taking the average of the three technical replicates.
- Calculated the t-stat for each gene in a new column by taking the average of the three biological replicates divided by (the standard deviation of the biological replicates divided by the sq. root of the sample size (which was three) )
- Calculated the p-value in a new column by using Excel's TDIST function where the three entries were the absolute value of the t-stat, 2, and 2.
- Took an average FC for each of the three biological replicates.
- Copied into a new page titled forGenMAPP and inserted column 2 (System Code) where N was entered for each row.
Tu 10/15/2013
- Downloaded GenMAPP, my text files, and the 2009 Vibrio cholerae Gene Database
- Set the database to the downloaded 2009 Vibrio cholerae Gene Database
- In Expression Dataset Manager, created a new dataset by importing my txt for GenMAPP File
772 errors while creating a new dataset; errors in dataset or just could not find IDs
- in the exception file reported that the gene was not found, confirmed this was the case for all 772 errors by filtering
comparing to zero which is the null hypothesis of no change.
1) magnitude of change observing
2) variation and number of replicates
