Difference between revisions of "Malverso Week 8"

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(recorded color labels.)
m (did sanity checks)
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[[File:Merrell_Compiled_Raw_Data_Vibrio_MA_20151015_(2).EX.txt]]
 
[[File:Merrell_Compiled_Raw_Data_Vibrio_MA_20151015_(2).EX.txt]]
  
−
==Sanity Check==
+
==Sanity Check: Number of Genes Significantly Changed==
−
*Number of Genes with a p value less than .05 = 5187
+
*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 signifficant 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
 +
*VC0051 didnt have
 +
*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
 +
 
  
  

Revision as of 19:17, 25 October 2015

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 signifficant 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
  • VC0051 didnt have
  • 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

Heavy Metal HaterZ

Assignments

Individual Journal Entries

Shared Journal Entries

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