# Elizabeth Polidan Week9

### From OpenWetWare

(Difference between revisions)

## Revision as of 12:59, 2 April 2013

**Elizabeth Polidan**

BIOL 398.03 / MATH 388

- Loyola Marymount University

- Los Angeles, CA, USA

- Begin by recording in your wiki the number of replicates for each time point in your data.
- Sanity Check: Number of genes significantly changed
- Check the number of genes significantly changed
- How many genes have p value < 0.05?
- What about p < 0.01?
- What about p < 0.001?
- What about p < 0.0001?

- Bonferroni correction
- Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.

- Magnitude and direction of gene expression
- 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?
- 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?
- Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
- How many have an average log fold change of < -0.25 and p < 0.05? (These are 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.)

- Check expression of NSR1. Find NSR1 in your dataset.
- Is its expression significantly changed at any timepoint?
- Record the average fold change and p value for NSR1 for each timepoint in your dataset.

- Check for gene with smallest p-value. You can find this by sorting your data based on p value (but be careful that you don't cause a mismatch in the rows of your data!)
- Which gene has the smallest p value in your dataset (at any timepoint)?
- Look up the function of this gene at the Saccharomyces Genome Database and record it in your notebook.
- Why do you think the cell is changing this gene's expression upon cold shock?

- Check the number of genes significantly changed