'top50 & reg' 'Block-Prior' Average Show

Download: PDF/JPG

Data: vsn-normalization.xls 'Control' Data

Setting:
murange = [0 .1 .5 1 2 4 8 12 16 32 64 100];
10 seeds for vbssm model training

Procedures:
1. Sort 'top50 & reg' as blocks: pdf / xls
2. In k-th experiment, incoporate blocks[1:k] as prior, take the average of 10 seeds for significance computation
3. Analyze the recovered true arcs, Total # = 10.
They are grouped into 2 catogaries: tdcA-arcs & tdcR-arcs, where:

tdcA-arcs: (color is agree with legend)

tdcA pd tdcB

tdcA pd tdcC
tdcA pd tdcD
tdcA pd tdcE
tdcA pp tdcA

tdcR-arcs: (color is agree with legend)

tdcR pp tdcA

tdcR pp tdcB
tdcR pp tdcC
tdcR pp tdcE
tdcR pp tdcD

More details about this work
1. Sort the 'top50 & reg' as blocks.
That means, arcs with same 'from-gene' are grouped as one block, ignore the 'to-gene'.
E.g. The group containing all tdcA-arcs are named block-1, the group containing all tdcR-arcs are named block-2.
block-idx from to

1	tdcA	tdcA
1	tdcA	tdcB
1	tdcA	tdcD
1	tdcA	tdcE
1	tdcA	tdcF
1	tdcA	tdcG
1	tdcA	tdcC

2	tdcR	tdcA
2	tdcR	tdcB
2	tdcR	tdcC
2	tdcR	tdcE
2	tdcR	tdcF
2	tdcR	tdcG
2	tdcR	tdcD

>From block-3, block-index is numbered by the alphabet order of 'from-genes'

2. Add prior for vbssm training.
There are 29 experiment, since the block # I sort in 'top50®' is exactly 29. Each experiment also explores mu range.
1st test, add all tdcA-arcs (i.e. block-1) as prior
2nd test, keep the tdcA-arcs (block-1) as prior, meanwhile add tdcR-arcs (block-2) as prior.
....
29th test, all arcs (i.e. block(1:29) ) are added as priors.

3. Organize the 29 experiment data, each murange = [0 .1 .5 1 2 4 8 12 16 32 64 100]
Since mu value play an important role in recovery evaluation, I made the figure to reflect this point.

There is no true network at hand, only 10 known arcs. I named them as 2 groups
tdcA-arcs:(from gene = tdcA, to gene = don't care)
tdcA pd tdcB
tdcA pd tdcC
tdcA pd tdcD
tdcA pd tdcE
tdcA pp tdcA

tdcR-arcs:(from gene = tdcR, to gene = don't care)
tdcR pp tdcA
tdcR pp tdcB
tdcR pp tdcC
tdcR pp tdcE
tdcR pp tdcD

Different colors, blue and pink, to demonstrate 10 true arcs recovery results. Blue = tdcA-arcs, pink = tdcR-arcs.
The bule+pink stack gives the total number of vbssm identified true arcs.

Based on my understanding, figure revealed at least 2 information:
1. mu = 0.5 is optimum mu value, at which # of recovered arcs reaches peak.
2. In global view, pink-arcs only showed with some special mu, whileas, blue-arcs are not significantly affected by mu value.