Hanie's lab notebook 2

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

Daily Summary:


inetgrator
General plan, microarray2symbol
Thesis presentation
Abstract


2018-08-20
The RnBeads package has so many dependency packages that uses a huge amount of space. To create a mini package from the RnBeads package, I have to summarize some of its functions that I used in the RnBeads.R script. In the new mini RnBeads package, I will omit some of original features of the RnBeads such as html reports and plots.

2018-08-08
How to Increase the R_MAX_NUM_DDL in R


2018-07-22

Studied for the midterm exam: software engineering.
Read a paper.
Started to write the compute.inetgrate function.


2018-07-21
I wrote the combined.eigengene function. When we edited the function during the lab meeting, we copied and pasted one of the formulas in the wrong place. That's why when I computed eigengenes again, I got an error:

Error in oneway.test(data = Data, formula = f1) : not enough groups
So I checked everything and found that eigengenes were all 0 since the lambda formula was wrong. I fixed the formula and also the survival fucntion.




2018-07-11

"tasks : expr_dnam_union took :"

Time difference of 2.420175 hours





2018-07-10
Working on my thesis, Fixed issues mentioned by proofreader
Working as GIA


2018-07-06,7,8

Summer camp
Working on my thesis: fixing issues that Dr. Metsis mentioned.


2018-07-05
Working on my thesis: fixing issues that Dr. Lewis mentioned.



2018-07-04
No update!



2017-07-03
Thesis presentation

2018-06-24
I wrote pathway analysis and validation. I fixed some parts of the lsc script (still does not work) + AFT script (To fix km plots and the thresholds plots) .


2018-06-19,20
Finished network +Wrote some about survival + i have to fix km plots for survival + wrote about LSC17 + i am going to write about Gerstung today.
Validation is remained


2018-06-17
Wrote results: network analysis+ part of survival


2018-06-16

2018-06-15
Survival analysis


2018-06-10


2018-06-8,9
Thesis: method section : data preparation, network analysis+introduction


2018-06-6,7
Thesis: method section: data preparation


2018-06-4,5
Thesis:
I worked on the general format of the thesis, overview of the implemented methodology and the FEM method.
TED :Let's pool our medical data
open source cancer research



2018-05-27,26
Working on my thesis using provided tex format by the grad college. I should create a git repository and upload my documents.


2018-05-14
Working on my proposal


2018-04-03 : 2018-05-13
Final exams and projects
2018-04-29
Applying for job
Studying for Database systems final exam


2018-04-28
-----------

2018-04-27
Database sytems project
meeting with Dr. Ngu
meeting with Dr. Metsis



2018-04-26
Databse systems project
meeting with Dr. Ngu for independent study, preparing forms
Formal interview for GIA



2018-04-22

applied for job

AI project

sv
I checked all emails contained pigengenes. Last time that Dr. Zare changed the pigengene regrads ro eigengenes was october.

also, I reran the pipeline with lambda =0.6 with task=network. Then i reran pipeline with pigengen 1.3.8 and task=eigengene. The problem is that the geneProjected object is different with both Dr. Zare's and my original object.



2018-04-21
AI Project

database systems project.



2018-04-20


AI Project


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