Difference between revisions of "Kmeilak Week 8"
From LMU BioDB 2013
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*Copied all data from compiled_raw_data worksheet into scaled_centered worksheet | *Copied all data from compiled_raw_data worksheet into scaled_centered worksheet | ||
*Inserted two rows underneath header row (ID, A1, etc) | *Inserted two rows underneath header row (ID, A1, etc) | ||
| − | *Calculated average and standard deviation for each column | + | *Calculated average and standard deviation for each column {i.e. =AVERAGE(B4:B5224); =STDEV(B4:B5224)} by typing function into appropriate labeled row and copying and pasting formulas across all columns. |
| + | *Calculated the scaled centered values by subtracting the average value for each column from the value in each and dividing by the standard deviation {i.e. (=B4-B$2)/B$3} | ||
| + | *Inserted a new worksheet and named it "statistics". | ||
| + | *Copied and pasted all of scaled_centered worksheet into statistics worksheet (note: did paste special values only). | ||
| + | *Added three new columns: "Avg_LogFC_A", "Avg_LogFC_B", "Avg_LogFC_C" | ||
| + | *Computed average log fold change {i.e. =AVERAGE(B2:E2)} for all patients | ||
| + | *Computed average of averages of three patients in new column titled "Avg_LogFC_all" | ||
| + | *Created a new column titled "Tstat" in order to run a T test using the following equation {=AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(number of replicates))}. The T test was run in order to see which, if any, of the scaled and centered average log ratios are significantly different from 0 (no change). | ||
| + | *Created a new column titled "Pvalue". Calculated P value using the following equation {=TDIST(ABS(R2),degrees of freedom,2)} | ||
| + | *Created a new worksheet titled "forGENMAPP". | ||
| + | *Copied and pasted everything in "statistics" worksheet into "forGENMAPP" worksheet. | ||
| + | |||
10/15/13 | 10/15/13 | ||
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#cellular nitrogen compound metabolic process | #cellular nitrogen compound metabolic process | ||
#cellular amine metabolic process | #cellular amine metabolic process | ||
| + | |||
| + | Questions | ||
| + | |||
| + | 1. | ||
==Files== | ==Files== | ||
Revision as of 03:19, 16 October 2013
Overview of Microarray Data Analysis
Electronic Lab Notebook
10/10/13
- Downloaded Merrill Compiled Raw Data file from Sample Microarray Analysis for Vibrio cholerae page
- Saved as Merrell_Compiled_Raw_Data_Vibrio_KM_20131010.xls
- Opened file in excel; created second worksheet and named it scaled_centered
- Copied all data from compiled_raw_data worksheet into scaled_centered worksheet
- Inserted two rows underneath header row (ID, A1, etc)
- Calculated average and standard deviation for each column {i.e. =AVERAGE(B4:B5224); =STDEV(B4:B5224)} by typing function into appropriate labeled row and copying and pasting formulas across all columns.
- Calculated the scaled centered values by subtracting the average value for each column from the value in each and dividing by the standard deviation {i.e. (=B4-B$2)/B$3}
- Inserted a new worksheet and named it "statistics".
- Copied and pasted all of scaled_centered worksheet into statistics worksheet (note: did paste special values only).
- Added three new columns: "Avg_LogFC_A", "Avg_LogFC_B", "Avg_LogFC_C"
- Computed average log fold change {i.e. =AVERAGE(B2:E2)} for all patients
- Computed average of averages of three patients in new column titled "Avg_LogFC_all"
- Created a new column titled "Tstat" in order to run a T test using the following equation {=AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(number of replicates))}. The T test was run in order to see which, if any, of the scaled and centered average log ratios are significantly different from 0 (no change).
- Created a new column titled "Pvalue". Calculated P value using the following equation {=TDIST(ABS(R2),degrees of freedom,2)}
- Created a new worksheet titled "forGENMAPP".
- Copied and pasted everything in "statistics" worksheet into "forGENMAPP" worksheet.
10/15/13
- Opened
Top 10 Gene Ontology terms
- macromolecule metabolic process
- cellular macromolecule metabolic process
- marcomolecule biosynthesis process
- biopolymer metabolic process
- cell projection organization
- branched chain family amino acid metabolic process
- amino acid metabolic process
- cellular amino acid and derivative metabolic process
- cellular nitrogen compound metabolic process
- cellular amine metabolic process
Questions
1.
