# Difference between revisions of "Elizabeth Polidan Week9"

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.

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t30

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t60

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t90

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t120
4

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4

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4

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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?
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t15

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t30

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t60

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t90

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<.05

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802

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1213

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1046

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672

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288
<.01

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202

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415

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276

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162

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36
<.001

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24

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69

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33

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14

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5
<.0001

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2

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8

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4

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0

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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.
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p

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t15

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t30

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t60

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t90

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t120
<.05

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0

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1

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0

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0

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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?