Ntesfaio Week 8

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 6.87

For T30 the average Log was 3.86

For T60 the average Log was 3.65

For T90 the average Log was 60.67

For T120 the average Log was 6.998

Does NSR1 change expression due

to cold shock in this experiment?

Data & Files

Media:Copy of BIOL367 F19 microarray-data dHAP4NtesfaioNT.zip

Powerpoint Slide

Acknowledgments

My homework partners this week are Aby User:Ymesfin and David User:Dramir36. We sat together in class to go over the assignment.