Knguye66 Week 7

Microrray Data Analysis (wild type data)

Background

Sanity Check

- The number of genes that are significantly changed at p value cut-off of p < 0.05 -

• How many genes have p < 0.05? and what is the percentage (out of 6189)?
  • -
• How many genes have p < 0.01? and what is the percentage (out of 6189)?
  • -
• How many genes have p < 0.001? and what is the percentage (out of 6189)?
  • -
• How many genes have p < 0.0001? and what is the percentage (out of 6189)?
  • -

- Filter data to determine the following -

• How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?
  • -
• How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
  • -

- Compare your results with known data. Note that the average Log fold change is what we called "STRAIN)_AvgLogFC_(TIME)" in step 3 of the ANOVA analysis. Does NSR1 change expression due to cold shock in this experiment? -

• Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?
  • -

- Find your favorite gene from Week 3. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment? Does your favorite gene change expression due to cold shock in this experiment? -

• • -