Kasey E. O'Connor Week 9 Journal: Difference between revisions
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==Microarry Data Analysis== | ==Microarry Data Analysis== | ||
#The number of replicates for each time point in the data. | |||
#* | |||
#Why is the use of the dollar sign symbols in front of the number important?" | |||
#* | |||
#How many genes have p value < 0.05? | |||
#* | |||
#What about p < 0.01? | |||
#* | |||
#What about p < 0.001? | |||
#* | |||
#What about p < 0.0001? | |||
#* | |||
#How many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction? | |||
#* | |||
#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? | |||
#* | |||
#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. | |||
#* | |||
#Which gene has the smallest p value in your dataset (at any time point)? Why do you think the cell is changing this gene's expression upon cold shock? | |||
#* | |||
====Useful Links==== | ====Useful Links==== | ||
{{Kasey E. O'Connor}} | {{Kasey E. O'Connor}} |
Revision as of 22:21, 30 March 2013
Microarry Data Analysis
- The number of replicates for each time point in the data.
- Why is the use of the dollar sign symbols in front of the number important?"
- How many genes have p value < 0.05?
- What about p < 0.01?
- What about p < 0.001?
- What about p < 0.0001?
- How many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction?
- 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?
- 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.
- Which gene has the smallest p value in your dataset (at any time point)? Why do you think the cell is changing this gene's expression upon cold shock?
Useful Links
- BIOL398-03/S13 Homepage
- Kasey E. O'Connor
- Shared Class Journals
- Kasey E. O'Connor Week 1 Shared Journal
- Kasey E. O'Connor Week 2 Shared Journal
- Kasey E. O'Connor Week 3 Shared Journal
- Kasey E. O'Connor Week 4 Shared Journal
- Kasey E. O'Connor Week 5 Shared Journal
- Kasey E. O'Connor Week 6 Shared Journal
- Kasey E. O'Connor Week 8 Shared Journal
- Kasey E. O'Connor Week 9 Shared Journal
- Kasey E. O'Connor Week 11 Shared Journal
- Kasey E. O'Connor Week 12 Shared Journal
- Kasey E. O'Connor Week 13 Shared Journal
- Kasey E. O'Connor Week 14 Shared Journal
- Individual Journal
- Kasey E. O'Connor Week 2 Journal
- Kasey E. O'Connor Week 3 Journal
- Kasey E. O'Connor Week 4 Journal
- Kasey E. O'Connor Week 5 Journal
- Kasey E. O'Connor Week 6 Journal
- Kasey E. O'Connor Week 8 Journal
- Kasey E. O'Connor Week 9 Journal
- Kasey E. O'Connor Week 11 Journal
- Kasey E. O'Connor Week 12 Journal
- Kasey E. O'Connor Week 13 Journal
- Kasey E. O'Connor Week 14 Journal
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