Kasey E. O'Connor Week 9 Journal

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Microarry Data Analysis

  1. The number of replicates for each time point in the data.
  2. Why is the use of the dollar sign symbols in front of the number important?"
  3. How many genes have p value < 0.05?
  4. What about p < 0.01?
  5. What about p < 0.001?
  6. What about p < 0.0001?
  7. How many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction?
  8. Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria?
  9. Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria?
  10. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
  11. How many have an average log fold change of < -0.25 and p < 0.05?
  12. Find NSR1 in your dataset. Is it's expression significantly changed at any timepoint? Record the average fold change and p value for NSR1 for each timepoint in your dataset.
  13. Which gene has the smallest p value in your dataset (at any time point)? Why do you think the cell is changing this gene's expression upon cold shock?

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