Difference between revisions of "Gleis Week 8"

Revision as of 05:41, 11 October 2013

Vibrio cholerae Statistical Analysis

Uploaded Files

File:ForGenMapp Gleis 10-10.txt

File:ForGenMapp Gleis 10-10.xls

Sanity Check

P<0.05 - 137

p<0.01 - 26

p<0.001 - 2

p<0.0001 - 0

p<0.05 and fold change>0 - 43

p<0.05 and fold change<0 - 94

p<0.05 and fold change>0.25 - 41

p<0.05 and fold change<-.025 - 93

Lab Journal

1. Visited https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Week_82 for procedural instructions

2. Opened this link: Sample Microarray Analysis for Vibrio cholerae page and downloaded data from Merrel et al. Host-induced epidemic spread of the cholera bacterium (2002)

3.Copied and selected all data in the file and pasted into a new Excel spreadsheet titled "Normalized".

4. Inserted two new rows just under the top title row. The first row was labeled "Average" and the second row was labeled "STDEV".

5. The average and standard deviations were calculated for each column

6. The data was then normalized by subtracting the average from a particular cell and dividing that sum by the standard deviation.

7. The data was copied and pasted-values only- into a new Excel sheet titled "statistics"

8. The averages of the technical replicates of each biological sample were calculated in the next three Columns

9. One column contained the average values of each gene for patient A, then Patient B, and finally patient C

10. In the next column the average values of A,B, and C were average to find a total average for each gene

11. Next a column was used to calculate if the average log ratio differed significantly from 0 using the equation

=AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(number of replicates))

12. Next a p-value was calculated for each gene using the equation

=TDIST(ABS(R2),degrees of freedom,2)

13. The data were then formatted to be accepted by GenMAPP.