# Difference between revisions of "Matthew E. Jurek Week 9"

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(→Sanity Check: deleted timepoints except for t30) |
(→Sanity Check: corrected last 4 questions) |
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Line 30: | Line 30: | ||

##t90= 0 | ##t90= 0 | ||

##t120= 0 | ##t120= 0 | ||

− | For the timepoint that had the greatest number of genes significantly changed at p < 0.05, answer the following: | + | #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 | ##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? | #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 | ##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? | #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 | ##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.) | #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 | ##t30= 198 | ||

+ | ##t60= 247 | ||

+ | ##t90= 63 | ||

+ | ##t120= 74 |

## Revision as of 18:10, 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