Amanda N. Wavrin Week 12

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Vibrio cholerae Microarray Presentation Assignment

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

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

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