Knguye66 Week 7

Notes before starting

• T-test -> is this gene expression change significantly different than zero?
• p<0.05: probability that you would have at least this big of a change by chance
  • ie. when we have 6189 genes, there are 6189 t-tests, are they significant? when we say there's a p<0.05, there's a 5% chance it's due to chance... meaning, if we have 6189 (5% of these are significant just by chance)
• magnitude of difference
• variation is sample measurements
• number of samples/measurements

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• ANOVA --> is the gene expression significantly different than zero at any time point?

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)?
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• How many genes have p < 0.01? and what is the percentage (out of 6189)?
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• How many genes have p < 0.001? and what is the percentage (out of 6189)?
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• How many genes have p < 0.0001? and what is the percentage (out of 6189)?
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- 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)?
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• How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
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- 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?
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- 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? -

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Acknowledgements

This section is in acknowledgement to partner Christina Dominguez (User:Cdomin12), as well as, Marcus Avila (User:Mavila9) and Jonar Cowan (User:Jcowan4).

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

User Page

User:knguye66

Template Page

Template:knguye66

Table of all assignments and journal entries for BIO-367-01

Week	Individual Journal Entry	Shared Journal
Week 1	-	Class Journal Week 1
Week 2	knguye66 Week 2	Class Journal Week 2
Week 3	ILT1/YDR090C Week 3	Class Journal Week 3
Week 4	knguye66 Week 4	Class Journal Week 4
Week 5	DrugCentral Week 5	Class Journal Week 5
Week 6	knguye66 Week 6	Class Journal Week 6
Week 7	knguye66 Week 7	Class Journal Week 7
Week 8	knguye66 Week 8	Class Journal Week 8
Week 9	knguye66 Week 9	Class Journal Week 9
Week 10	knguye66 Week 10	Class Journal Week 10
Week 11	knguye66 Week 11	FunGals
Week 12/13	knguye66 Eyoung20 Week 12/13	FunGals
Week 15	knguye66 Eyoung20 Week 15	Class Journal Week 15