Lab notebook 1
Todo.
My email is : hanie.samimi@gmail.com
ls5 scratch : /scratch/04431/h_s163

Daily Summary:


inetgrator
General plan, microarray2symbol

2018-04-18
Biochem presentation



2018-04-17
Facebook Tech-talk
There is a problem with reproducing results for TCGA data. We guess maybe it's because of the version of pigengene. Original objects are accesible from here and, i will work on it to figure out the isssue.


2018-04-15
Applied for jobs.
Biochem presentation.

2018-04-14
Tried to figure out the issue that happened while Dr. Zare was trying to reproduce survival results for tcga dataset. See his lano on 2018-04-14
Trying to find the issue with my ai-checkers script.

2018-04-13
Cs seminar: open source coding
AI project.

2018-04-11
Studied for the biochem final exam

2018-04-10
Studying for biochem final exam
Eigengenes are ready, next step will be survival

2018-04-08
AI-project and biochem midterm exam
pipeline: network is finished now.
paper:
applying for job and internship.


AI project.
2018-04-07


2018-04-04
Based on those changes that Dr. Zare made on libraries and also after installing pigenge version 1.4.20:
to detach all dependencies of a package from an R session :

>>to be continued

2018-04-03

database systems exam!


2018-04-02
error while runnig network again !


debug at ~/proj/genetwork/code/Hanie/NetworkAnalysis/dnam_expr/genExpression_dnam_network.R#93: netModule <- blockwiseModules(datExpr = eigenloci, saveTOMs = FALSE,
power = pstPower$powerEstimate, loadTOM = TRUE, maxBlockSize = maxBlockSize,
corType = "pearson", mergeCutHeight = 0.15, reassignThreshold = 1e-06,
networkType = "unsigned", replaceMissingAdjacencies = FALSE,
TOMType = "unsigned", TOMDenom = "min", minModuleSize = minModuleSize,
numericLabels = TRUE, verbose = TRUE)
Browse[3]>
Calculating module eigengenes block-wise from all genes
Error in (function (x, y = NULL, use = "everything", method = c("pearson", :
unused arguments (weights.x = NULL, weights.y = NULL, cosine = FALSE)
In addition: Warning message:
executing %dopar% sequentially: no parallel backend registered
Habil: The above will be resolved when Pigengene version 1.4.20 or higher is used. Also, I had to modify runall and libraries.R


2018-04-01
AI project part 2 : implementation of the checkers game.


2018-03-31
Database systems project.


2018-02-30
Nowruz presentation


2018-03-28
I fixed the clone/pull/push problem with the refs repository based on this forum:
first edit file "/etc/resolv.conf" if any line doesn't exist , add some dns following example *nameserver 8.8.8.8*nameserver 8.8.4.4 and try again...


2018-03-27
1)I was preparing for an internship interview
2)I reran dnam/runall.R with these tasks: loading, tasksRnBeads, genExpr, expr_dnam_union



2018-03-26
Concordance and p-value for Med-risk patient of Herold data, using LSC Vs. Network analysis


2018-03-25
Trying to reproduce the AML paper results


2018-03-24
DataBase systems projetc-part2