Difference between revisions of "Taur.vil Week 8"
From LMU BioDB 2013
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Uploaded Files: | Uploaded Files: | ||
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:[[Media:Vilgalys_2013_10_10_VibrioFileOne.txt|text]] | :[[Media:Vilgalys_2013_10_10_VibrioFileOne.txt|text]] | ||
:[[Media:Vilgalys_2013_10_10_VibrioFileOne.xls|excel]] | :[[Media:Vilgalys_2013_10_10_VibrioFileOne.xls|excel]] | ||
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| + | :[[Media:Vilgalys_2013_10_10_VibrioFileOne.EX.txt|Exceptions]] | ||
| + | :[[Media:Vilgalys_2013_10_10_VibrioFileOne.gex|Expression Dataset]] | ||
| + | :[[Media:DecreasedVibrio_2009_TV-Criterion1-GO.txt|GO results file]] | ||
| + | :[[Media:Vilgalys_2013_10_10_VibrioFileOne.EX.xls|GO w/ filter]] | ||
| + | :MAPP not done yet | ||
| + | :[[Media:Vilgalys_2013_10_10_VibrioFileOne.gmf|GO mapping file]] | ||
==Digital Notebook:== | ==Digital Notebook:== | ||
Revision as of 17:51, 15 October 2013
Uploaded Files:
Contents |
Document Files:
- Exceptions
- Expression Dataset
- GO results file
- GO w/ filter
- MAPP not done yet
- GO mapping file
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 reported, all of which were reported as gene not found (verified using excel filters)
- Created new color set (Pathogenic vs Lab)
- Selected increasing items as those which had an AvgLogFC change > 0.25 and a p-value less than 0.05. ([AvgLogFC_all]>0.25 AND [Pvalue]<0.05)
- Selected decreasing items using the same criteria, just an inversed AvgLogFC change ([AvgLogFC_all]<-0.25 AND [Pvalue]<0.05)
- Colored increased as red, decreases as green, and no change as yellow
- Used GenMAPP tool MAPPFinder to create a table for decreases in gene expression, exported as DecreasedVibrio_2009_TV.
want z to be high and positive, higher than 2 means p is less than .05
comparing to zero which is the null hypothesis of no change. 1) magnitude of change observing 2) variation and number of replicates
