LauraTerada Individual Journal Assignment Week 9

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(bonferroni correction answer)
Current revision (14:39, 2 April 2013) (view source)
 
(One intermediate revision not shown.)
Line 19: Line 19:
**4 genes have p < 0.0001
**4 genes have p < 0.0001
*t30
*t30
-
**492 genes have p value < 0.05
+
**946 genes have p value < 0.05
**266 genes have p < 0.01
**266 genes have p < 0.01
**34 genes have p < 0.001
**34 genes have p < 0.001
**6 genes have p < 0.0001
**6 genes have p < 0.0001
*t60
*t60
-
**284 genes have p value < 0.05
+
**1006 genes have p value < 0.05
**274 genes have p < 0.01
**274 genes have p < 0.01
**35 genes have p < 0.001
**35 genes have p < 0.001
Line 44: Line 44:
**t90: 0 genes
**t90: 0 genes
**t120: 1 gene
**t120: 1 gene
 +
*t15 had the most genes with a p value <0.05
 +
**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?
 +
***613 genes
 +
**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?
 +
***861 genes
 +
**Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
 +
***600 genes
 +
**How many have an average log fold change of < -0.25 and p < 0.05?
 +
***815 genes
 +
*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.
 +
**average fold changes for:
 +
***t15: 2.04
 +
***t30: 2.21
 +
***t60: 2.43
 +
***t90: -1.59
 +
***t120: -0.56
 +
**p values for:
 +
***t15: 0.0174
 +
***t30: 0.0320
 +
***t60: 0.0020
 +
***t90: 0.0102
 +
***t120: 0.2257
 +
***All time points, except for t120, were significantly changed with a p value <0.01
 +
*Which gene has the smallest p value in your dataset (at any timepoint)?
 +
**AIM25/YJR100C function: putative protein of unknown function
 +
*Why do you think the cell is changing this gene's expression upon cold shock?
 +
**Unknown because it has an unknown function; however, the database says that it can be detected in mitochondria. Perhaps AIM25 has a role in respiration under cold shock conditions.

Current revision

  • Replicates for each time point
    • 15C: 4
    • 30C: 4
    • 60C: 4
    • 90C: 4
    • 120C: 4
  • We use the dollar sign symbols in front of the number to tell Excel to always reference that row in the equation, even though we will paste it for the entire column. Why is this important?
    • If you paste it through the entire column without the dollar sign, the box that you want for each equation won't normalize and it will be different for each equation. You need the dollar sign to keep the same box in each equation throughout the column.
  • Scan through your spreadsheet to find an example of the error message. Then go to the Edit menu and Select Replace. A window will open, type the text you are replacing in the "Find what:" field. In the "Replace with:" field, enter a single space character. Click on the button "Replace All" and record the number of replacements made in your wiki page.
    • No error messages.
  • t15
    • 1474 genes have p value < 0.05
    • 345 genes have p < 0.01
    • 30 genes have p < 0.001
    • 4 genes have p < 0.0001
  • t30
    • 946 genes have p value < 0.05
    • 266 genes have p < 0.01
    • 34 genes have p < 0.001
    • 6 genes have p < 0.0001
  • t60
    • 1006 genes have p value < 0.05
    • 274 genes have p < 0.01
    • 35 genes have p < 0.001
    • 0 genes have p < 0.0001
  • t90
    • 732 genes have p value < 0.05
    • 190 genes have p < 0.01
    • 12 genes have p < 0.001
    • 1 gene have p < 0.0001
  • t120
    • 397 genes have p value < 0.05
    • 89 genes have p < 0.01
    • 9 genes have p < 0.001
    • 1 gene have p < 0.0001
  • 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 genes
    • t30: 0 genes
    • t60: 0 genes
    • t90: 0 genes
    • t120: 1 gene
  • t15 had the most genes with a p value <0.05
    • 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?
      • 613 genes
    • 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?
      • 861 genes
    • Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
      • 600 genes
    • How many have an average log fold change of < -0.25 and p < 0.05?
      • 815 genes
  • 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.
    • average fold changes for:
      • t15: 2.04
      • t30: 2.21
      • t60: 2.43
      • t90: -1.59
      • t120: -0.56
    • p values for:
      • t15: 0.0174
      • t30: 0.0320
      • t60: 0.0020
      • t90: 0.0102
      • t120: 0.2257
      • All time points, except for t120, were significantly changed with a p value <0.01
  • Which gene has the smallest p value in your dataset (at any timepoint)?
    • AIM25/YJR100C function: putative protein of unknown function
  • Why do you think the cell is changing this gene's expression upon cold shock?
    • Unknown because it has an unknown function; however, the database says that it can be detected in mitochondria. Perhaps AIM25 has a role in respiration under cold shock conditions.
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