Matthew E. Jurek Week 9

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(Sanity Check: prepped next set of questions)
(Sanity Check: answered next set of questions)
Line 24: Line 24:
##t90= 1
##t90= 1
##t120= 0
##t120= 0
-
#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 less than zero. How many meet these two criteria?
 
-
#Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
 
-
#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.)
 
#Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.
#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  
##t15= 0  
Line 34: Line 30:
##t90= 0  
##t90= 0  
##t120= 0
##t120= 0
 +
#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

Revision as of 20:55, 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
  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?
    1. t15= 203
    2. t30= 332
    3. t60= 168
    4. t90= 118
    5. t120= 104
  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?
    1. t15= 182
    2. t30= 212
    3. t60= 266
    4. t90= 86
    5. t120= 86
  8. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
    1. t15= 0
    2. t30= 0
    3. t60= 0
    4. t90= 0
    5. t120= 0
  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.)
    1. t15= 150
    2. t30= 198
    3. t60= 247
    4. t90= 63
    5. t120= 74
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