Difference between revisions of "Malverso Week 8"
From LMU BioDB 2015
m (did sanity checks) |
(completed sanity checks) |
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* > .25 = 339. 17.83% | * > .25 = 339. 17.83% | ||
* <-.25 = 579. 11.09% | * <-.25 = 579. 11.09% | ||
| − | *"two-class SAM analysis was conducted" "with statistically significant changes in the level of expression - at least a twofold change" They used the actual level of expression change to figure out what was | + | *"two-class SAM analysis was conducted" "with statistically significant changes in the level of expression - at least a twofold change" They used the actual level of expression change to figure out what was significant while we used p value (which is the probability that changes in expression are due to chance). Merrell et al. (2002) used a more stringent method because they found 237 genes that were significantly changed while we found 918. (-.25 < pvalue > .25) |
==Sanity Check: Compare Individual Genes with Known Data== | ==Sanity Check: Compare Individual Genes with Known Data== | ||
| Line 26: | Line 26: | ||
*first is sig changed, second is not | *first is sig changed, second is not | ||
*VC0941 -.28 .1636 and .88 .0001 | *VC0941 -.28 .1636 and .88 .0001 | ||
| − | *VC0869 | + | *VC0869 Fold changes: 2.12, 1.50, 1.59, 1.95, 2.20 |
| − | *VC0051 | + | P value: 0.02, 0.0174, 0.0463, 0.0227, 0.002 |
| + | All are significantly changed | ||
| + | *VC0051 Fold change: 1.89, 1.92 | ||
| + | P value: 0.016, 0.0139 | ||
| + | Both are significantly changed | ||
*VC0647 fold change: -1.11 pvalue:.0003 and fold change:-0.94 pvalue:.0125 and fold change:-1.05 pvalue:.0051 | *VC0647 fold change: -1.11 pvalue:.0003 and fold change:-0.94 pvalue:.0125 and fold change:-1.05 pvalue:.0051 | ||
*VC0468 -.17 and pvalue:.3350 | *VC0468 -.17 and pvalue:.3350 | ||
Revision as of 19:20, 25 October 2015
Contents
Files:
File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).xls
File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).txt
File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).gex
File:Merrell Compiled Raw Data Vibrio MA 20151015 (2).EX.txt
Sanity Check: Number of Genes Significantly Changed
- Number of genes with a p value less than .05 = 948. This is 18.16% of the genes.
- Number of genes with a p value less than .01 = 235. This is 4.50% of the genes.
- Number of genes with a p value less than .001 = 24. This is 0.46% of the genes.
- Number of genes with a p value less than .0001 = 2. This is 0.04% of the genes.
- Number of genes with a Bonferroni p value less than .05 = 0. This is 0% of the genes.
- Number of genes with a B-H p value less than .05 = 0. This is 0% of the genes.
- Avg_LogFC_all > 0 = 352. 6.7%
- < 0 = 596. 11.34%
- > .25 = 339. 17.83%
- <-.25 = 579. 11.09%
- "two-class SAM analysis was conducted" "with statistically significant changes in the level of expression - at least a twofold change" They used the actual level of expression change to figure out what was significant while we used p value (which is the probability that changes in expression are due to chance). Merrell et al. (2002) used a more stringent method because they found 237 genes that were significantly changed while we found 918. (-.25 < pvalue > .25)
Sanity Check: Compare Individual Genes with Known Data
- VC0028 fold change: 1.65 pvalue:.0474 and 1.27 .0692
- first is sig changed, second is not
- VC0941 -.28 .1636 and .88 .0001
- VC0869 Fold changes: 2.12, 1.50, 1.59, 1.95, 2.20
P value: 0.02, 0.0174, 0.0463, 0.0227, 0.002 All are significantly changed
- VC0051 Fold change: 1.89, 1.92
P value: 0.016, 0.0139 Both are significantly changed
- VC0647 fold change: -1.11 pvalue:.0003 and fold change:-0.94 pvalue:.0125 and fold change:-1.05 pvalue:.0051
- VC0468 -.17 and pvalue:.3350
- VC2350 fold change: -2.40 pvalue:.0130
- VCA0583 fold change: 1.06 pvalue: .1011
Part Two
- I used the 2010 database.
- There were 121 errors.
- Kristin used the 2009 database and 772 errors were detected.
- We were an increased pair, which I labeled red.
- I labeled decreased wih green.
Team Page
Assignments
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 13
- Week 14
- Week 15
Individual Journal Entries
- Malverso User Page (Week 1)
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 13
- Week 14
- Week 15
