# Difference between revisions of "Anthony J. Wavrin Week 9"

## Assignment 9

File of the spreadsheet with the statistics for dHMO1 is uploaded on Lionshare.

1. How many genes have p value < 0.05?

Time # of genes
15 385
30 544
60 434
90 204
120 190

2. What about p < 0.01?

Time # of genes
15 81
30 108
60 87
90 28
120 34

3. What about p < 0.001?

Time # of genes
15 8
30 10
60 6
90 5
120 4

4. What about p < 0.0001?

Time # of genes
15 0
30 1
60 1
90 1
120 0

5. Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.

• There were no genes at any time point that has a p value < 0.05 after the Bonferroni correction.

6. 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?

• 332

7. 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?

• 212

8. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?

• 306

9. 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.)

• 198

10.Find NSR1 in your dataset. Is it's expression significantly changed at any timepoint? Record the average fold change and p value for NSR1 for each timepoint in your dataset.

• There were no time points that had "significiantly" changed but, some time points were close to a p value of 0.05.
Time Avg Fold Change P Value
15 0.91 0.0385
30 1.19 0.0722
60 1.26 0.1618
90 -0.24 0.5704
120 -0.25 0.5507