Matthew E. Jurek Week 9: Difference between revisions
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##t120= 74 | ##t120= 74 | ||
#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. | #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. | ||
##Fold Change | |||
###t15= .91 | |||
###t30= 1.19 | |||
###t60= 1.26 | |||
###t90= -.74 | |||
###t120= -.25 | |||
##P Value | |||
###t15= .0385 | |||
###t30= .0722 | |||
###t60= .1618 | |||
###t90= .5704 | |||
###t120= .5507 |
Revision as of 19:23, 2 April 2013
Sanity Check
- How many genes have p value < 0.05?
- t15= 385
- t30= 544
- t60= 434
- t90= 231
- t120= 190
- What about p < 0.01?
- t15= 81
- t30= 108
- t60= 87
- t90= 28
- t120= 34
- What about p < 0.001?
- t15= 8
- t30= 10
- t60= 6
- t90= 5
- t120= 4
- What about p < 0.0001?
- t15= 0
- t30= 1
- t60= 1
- t90= 1
- t120= 0
- Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.
- t15= 0
- t30= 0
- t60= 0
- t90= 0
- t120= 0
- For the timepoint that had the greatest number of genes significantly changed at p < 0.05, answer the following: Following the correction, there were no p values <.05. Thus, the following are calculations for each time point.
- 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?
- t15= 203
- t30= 332
- t60= 168
- t90= 118
- t120= 104
- 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?
- t15= 182
- t30= 212
- t60= 266
- t90= 86
- t120= 86
- Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
- t15= 0
- t30= 0
- t60= 0
- t90= 0
- t120= 0
- 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.)
- t15= 150
- t30= 198
- t60= 247
- t90= 63
- t120= 74
- 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.
- Fold Change
- t15= .91
- t30= 1.19
- t60= 1.26
- t90= -.74
- t120= -.25
- P Value
- t15= .0385
- t30= .0722
- t60= .1618
- t90= .5704
- t120= .5507
- Fold Change