Difference between revisions of "Blitvak Week 8"
From LMU BioDB 2015
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| − | == | + | ==Statistical Analysis of ''Vibrio cholerae'' Microarray Data (Part 1)== |
| − | + | *[http://www.openwetware.org/images/d/d6/Merrell_Compiled_Raw_Data_Vibrio.xls Merrell_Compiled_Raw_Data_Vibrio.xls] was downloaded, saved to the desktop, and renamed with some additional information (initials and the date) | |
| − | + | ===Normalizing the log ratios for the set of slides in the experiment=== | |
| − | *[http://www.openwetware.org/images/d/d6/Merrell_Compiled_Raw_Data_Vibrio.xls Merrell_Compiled_Raw_Data_Vibrio.xls] was downloaded and | + | The following operations were performed in order to scale and center the microarray data: |
| − | * | + | *The renamed Excel file was opened and a new Worksheet was inserted with the name ''scaled_centered'' |
| + | *Everything on the ''compiled_raw_data'' worksheet was selected and copied over to ''scaled_centered'' (formatting was the same, starting from the left-hand cell, A1) | ||
| + | *Two new rows were inserted between the top row of headers and the first data row in ''scaled_centered'' | ||
| + | *In cell A2, ''Average'' was typed in; in A3, ''StdDev'' was typed in. | ||
| + | *The Average log ratio for each chip was computed by typing <code>=AVERAGE(B4:B5224)</code> into cell B2 and pressing enter | ||
| + | *The Standard Deviation of the log ratios on each chip was computed by typing <code>=STDEV(B4:B5224)</code> into cell B3 and pressing enter | ||
| + | *The equations in B2 and B3 were copied and pasted into the empty cells in the rest of the columns (A2 to C4) | ||
| + | *The column headings for all of the data columns were copied and pasted to the right of the last data column; this new set of headers was edited so that they read: ''A1_scaled_centered, A2_scaled_centered'', etc.'' | ||
*[[Media:Merrell_Compiled_Raw_Data_Vibrio_BL_20151015.xls|Modified Excel File/Data]] | *[[Media:Merrell_Compiled_Raw_Data_Vibrio_BL_20151015.xls|Modified Excel File/Data]] | ||
Revision as of 03:30, 24 October 2015
Contents
Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)
- Merrell_Compiled_Raw_Data_Vibrio.xls was downloaded, saved to the desktop, and renamed with some additional information (initials and the date)
Normalizing the log ratios for the set of slides in the experiment
The following operations were performed in order to scale and center the microarray data:
- The renamed Excel file was opened and a new Worksheet was inserted with the name scaled_centered
- Everything on the compiled_raw_data worksheet was selected and copied over to scaled_centered (formatting was the same, starting from the left-hand cell, A1)
- Two new rows were inserted between the top row of headers and the first data row in scaled_centered
- In cell A2, Average was typed in; in A3, StdDev was typed in.
- The Average log ratio for each chip was computed by typing
=AVERAGE(B4:B5224)into cell B2 and pressing enter - The Standard Deviation of the log ratios on each chip was computed by typing
=STDEV(B4:B5224)into cell B3 and pressing enter - The equations in B2 and B3 were copied and pasted into the empty cells in the rest of the columns (A2 to C4)
- The column headings for all of the data columns were copied and pasted to the right of the last data column; this new set of headers was edited so that they read: A1_scaled_centered, A2_scaled_centered, etc.
Working with: 2009 Vibrio Cholera database
- 772 errors were detected in the raw data by genMAPP using the 2009 database
- 121 errors were detected in the raw data by genMAPP using the 2010 database by my partner, Anindita V.
Results of 10/20 Work Session
Results of 10/22 Work Session
- Top 10 Ranked GO Terms
- macromolecule metabolic process
- localization
- transporter activity
- cellular macromolecule metabolic process
- transport
- establishment of localization
- cell projection organization
- cellular biopolymer metabolic process
- macromolecule biosynthetic process
- biopolymer metabolic process
- Analysis of the .EX.txt file produced by GenMAPP, via Excel, revealed that the 772 errors were: Gene not found in OrderedLocusNames or any related system; this suggests that the 2009 database did not
increased expression
Brandon Litvak
BIOL 367, Fall 2015
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