Anthony J. Wavrin Week 9: Difference between revisions

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==Assignment 9==
==Assignment 9==
File of the spreadsheet with the statistics for dHMO1 is uploaded on Lionshare.
File of the spreadsheet with the statistics for dHMO1 is uploaded on Lionshare.
#How many genes have p value < 0.05?
 
1. How many genes have p value < 0.05?
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#What about p < 0.01?
2. What about p < 0.01?
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#What about p < 0.001?
3. What about p < 0.001?
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#What about p < 0.0001?
4. What about p < 0.0001?
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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




Revision as of 23:09, 2 April 2013

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



Original Assignment

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