Malverso Week 8

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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)

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