Matthew E. Jurek Week 9

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(Sanity Check: answered next set of questions)
(Sanity Check: deleted timepoints except for t30)
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:
#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?
#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 21:59, 2 April 2013

Sanity Check

  1. How many genes have p value < 0.05?
    1. t15= 385
    2. t30= 544
    3. t60= 434
    4. t90= 231
    5. t120= 190
  2. What about p < 0.01?
    1. t15= 81
    2. t30= 108
    3. t60= 87
    4. t90= 28
    5. t120= 34
  3. What about p < 0.001?
    1. t15= 8
    2. t30= 10
    3. t60= 6
    4. t90= 5
    5. t120= 4
  4. What about p < 0.0001?
    1. t15= 0
    2. t30= 1
    3. t60= 1
    4. t90= 1
    5. t120= 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.
    1. t15= 0
    2. t30= 0
    3. t60= 0
    4. t90= 0
    5. t120= 0

For the timepoint that had the greatest number of genes significantly changed at p < 0.05, answer the following:

  1. 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?
    1. t30= 332
  2. 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?
    1. t30= 212
  3. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
    1. t30= 0
  4. 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.)
    1. t30= 198
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