Matthew E. Jurek Week 9

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(Sanity Check: typed NSR1 question)
(Sanity Check: answered NSR1 question)
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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 21:23, 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. 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.
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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.
    1. Fold Change
      1. t15= .91
      2. t30= 1.19
      3. t60= 1.26
      4. t90= -.74
      5. t120= -.25
    2. P Value
      1. t15= .0385
      2. t30= .0722
      3. t60= .1618
      4. t90= .5704
      5. t120= .5507
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