Ntesfaio Week 8
Contents
Electronic Workbook
Purpose
The purpose of this week's lab is to continue off of week 7 by going through the steps of the data life cycle for a DNA microarray dataset
Methods/ Results
Week 8 Interim deadline for excel spreadsheet
File:Copy of BIOL367 F19 microarray-data dHAP4NtesfaioNT.zip
How many genes have p < 0.05? and what is the percentage (out of 6189)?
2479/ 6189 or 40%
How many genes have p < 0.01? and what is the percentage (out of 6189)?
1583/ 6189 or 26%
How many genes have p < 0.001? and what is the percentage (out of 6189)?
739/ 6189 or 12%
How many genes have p < 0.0001? and what is the percentage (out of 6189)?
280/6189 or 5%
How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?
75/ 6189 or 1.2%
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
1735/ 6189 or 28%
Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values?
Unadjusted it is .016 Bonferroni-corrected is 101.3 B-H corrected is .056
What is its average Log fold change at each of the timepoints in the experiment? Note that the average Log fold change is what we called "STRAIN)_AvgLogFC_(TIME)" in step 3 of the ANOVA analysis.
For T15 the average Log was 2.7
For T30 the average Log was 3.3
For T60 the average Log was 3.5
For T90 the average Log was -1.1
For T120 the average Log was -1.8
Does NSR1 change expression due
to cold shock in this experiment?
My favorite gene was RAD53 or YPL153C
The unadjusted value was .512
Bonferroni-corrected is 3172
B-H corrected is .649
For T15 the average Log was -.5476
For T30 the average Log was -.5768
For T60 the average Log was -.5764
For T90 the average Log was 1.050
For T120 the average Log was -.1536
Data & Files
Media:Copy of BIOL367 F19 microarray-data dHAP4NtesfaioNT.zip
Conclusion
Acknowledgments
My homework partners this week are Aby User:Ymesfin and David User:Dramir36. We sat together in class to go over the assignment.
