Amanda N. Wavrin Week 12

Normalizing the Log Ratios for the Set of Slides in the Experiment

 * Created a new excel sheet labeled scaled_centered
 * Copy and pasted the spreadsheet into the new scaled_centered sheet
 * Inserted two rows at the top below the headers
 * Added headers "Average" to cell A2 and "StdDev" to cell A3
 * Computed the average log ratio using the equation =AVERAGE(B4:B5224)
 * Computed the StdDev using equations such as =STDEV(B4:B5224)
 * Now will do the scaling and centering using these found values
 * Added "scaled_centered" columns after each column
 * Used the equation =(B4-$B$2)/$B$3, =(D4-$D$2)/$D$3, and so on

Performing Statistical Analysis on the Ratios

 * Added new worksheet labeked statistics
 * Used the new worksheet to compute the average log fold change for the replicates for each patient
 * Calculated the averages of the averages
 * Computed a T statistic to tell us whether the average log ratio is significantly different than 0
 * Calculated the Pvalue using the equation =TDIST(ABS(R2),degrees of freedom,2, Using 2 for the degrees of freedom
 * Inserted a new worksheet and labeled it "forGenMAPP"
 * Changed cells B to Q to 2 decimal places
 * Changed cells R through S to 4 decimal places
 * Then moved columns N through S
 * added SystemCode column

GenMAPP Workskeets

 * [[Media:Bioinformatics Merrell Compiled Raw Data Vibrio.txt|.txt file]]
 * [[Media:Bioinformatics Merrell Compiled Raw Data Vibrio.xls| Excel file]]

Sanity Check

 * Selected autofilter for the GenMAPP worksheet
 * Two genes have a p value less then .05
 * With the Avg_LogFC_all set to greater than 0 there are two genes
 * With the Avg_LogFC_all set to less than 0 there are no genes left
 * With the average log fold change set to >.25 or <-.25 are were two genes
 * In the Merrell et al. study they used the DNA microarray to analyze the vibrio genes. They considered at least a two fold change to be a statistically significant change.
 * Merrell et al. reported these genes as having been significantly changed:
 * Gene VC0028: p value of 0.329215968 and a fold change of 1.652615448
 * Gene VC0941: p value of 0.818557972 and a fold change of 0.093359611
 * Gene VC0869: p value of 0.453843078 and a fold change of 1.592137524
 * Gene VC0051: p value of 0.279910262 and a fold change of 1.921808516
 * Gene VC0647: p value of 0.368013349 and a fold change of -1.112615156
 * Gene VC0468: p value of 0.930118019 and a fold change of -0.168589663
 * Gene VC2350: p value of 0.164978526 and a fold change of -2.402891699
 * Gene VCA0583: p value of 0.24189621 and a fold change of 1.062812449