10:00 A – 9:30P, 11:00P – 12:55 A
STORM
- Finish O/N run on STORM2
STORM Analysis
- Launch Analysis of all fab7 data collected on STORM2 — now running on Cajal in small batches.
- Finish configuring local repo on TUCK to run analysis. Had to fix matlab core path files, no idea how these got screwed up on Tuck
- Launched all STORM3 collected fab7 data on TUCK.
- Switching and brightness clearly better on STORM3. Should compare no-quad-view:
- Monet crashed when trying to remote connect. Crashed data analysis on Tuck. (Cajal resumed correctly).
- Relaunched data analysis on Tuck.
Genomics
- Fixed bug in primer selection
- Need to Re-do probe design: pasting homology-free 20mers together to make 64mers is not a good approach for building homology free 64mers.
- Figuring out how to call R code from HHMt
Figuring out details of HHMt algorithm
- First PCA the 54 dimensional data-set down to 3 dimensions
- Apply the BauerWelch HHM model to the first 3 principle components (saves memory, should get same classes).
- Wrote R script
\Chromatin\Code\Functions\applyHHMt.R - Wrote Matlab wrapper script
\Chromatin\Code\Functions\SimulateColorData.m - Works!
- (class numbers are arbitrary, but the correspondence should be the same (i.e. class1 in true data may be class4 in simulation).
R-notes
- package for dealing with big data matrices in R
Coding to Do:
- Role out updated version of STORMfinder
- Need DemoData
- Need short tutorial
- Need screenshots
- Need link to STORMfinderBeta
- Role out STORMrenderBeta
- Need DemoData
- Need short tutorial
- Need screenshots