Kevin Wyllie Week 14

Electronic Lab Notebook

Statistical Analysis and Formatting

We looked at Dr. Dahlquist's comments on our prior worksheet to make a second attempt at processing and formatting for GenMAPP. Primarily, our biggest error in the the previous attempt was forgetting to account for the fact that each gene was spotted in (technical) quadruplicates.

• Dr. Dahlquist prepared a sheet for us to start with, which separated each quadruplicate of the genome across columns. So the ID column for the first technical replicate is in A1, followed by

Sanity Check

There are 7251 genes in the sheet.

• How many genes have p value < 0.05? And what is the percentage?
  • 4318, ~60%
• What about p < 0.01?
  • 2971, ~41%
• What about p < 0.001?
  • 1460, ~20%
• What about p < 0.0001?
  • 645, ~9%

• How many genes are p < 0.05 for the Bonferroni-corrected p value?
  • 179, ~2.4%
• How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value?
  • 609, ~8.4%

• "Pvalue" < 0.05, and "Biofilm_Tobramycin_ratio" > 0.
• "Pvalue" < 0.05, and "Biofilm_Tobramycin_ratio" > 0.

This is a more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology:

• "Biofilm_Tobramycin_ratio" > 0.25 and "Pvalue" < 0.05.
• "Biofilm_tobramycin_ratio" < -0.25 and "Pvalue" < 0.05.