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

Excel Spreadsheet

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

Excel Spreadsheet

Powerpoint Slide

Stem Profile

Conclusion

The purpose of this week's assignment was to go through a DNA microarray dataset and work with filtering p-values that are above or below a specific number. This lab also incorporated STEM which stands for Short Time-series Expression Miner. A Java program used for clustering, comparing, and visualizing short time series gene expression data from microarray experiements.