# Elizabeth Polidan Week9

(Difference between revisions)

## Revision as of 00:18, 3 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.

t15 t30 t60 t90 t120
4 4 4 5 5

Data errors replaced by single space: 108 occurences

Sanity Check

• Check the number of genes significantly changed. How many genes have p value < 0.05? p < 0.01? p < 0.001? p < 0.0001?
p t15 t30 t60 t90 t120
<.05 802 1213 1046 672 288
<.01 202 415 276 162 36
<.001 24 69 33 14 5
<.0001 2 8 4 0 2

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.
p t15 t30 t60 t90 t120
<.05 0 1 0 0 0

Only one gene was still significantly changed under this stringent 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?