User: Joe Kherery

gravatar for Joe Kherery
Joe Kherery30
Reputation:
30
Status:
New User
Location:
Last seen:
3 days, 4 hours ago
Joined:
5 months, 2 weeks ago
Email:
J***************@gmail.com

Posts by Joe Kherery

<prev • 27 results • page 1 of 3 • next >
0
votes
2
answers
152
views
2
answers
Comment: C: MicroRNA-target interactions databases
... Hey Kevin, Yes it was last updated in Apr / 2018. I already built an interaction graph using cytoscape, it was similar to yours. As a beginner, I try to use the easiest tools. And about the ComplexHemapmap R package, But I do not know if I will have much time to use it. My time to finalize this data ...
written 7 days ago by Joe Kherery30
0
votes
2
answers
152
views
2
answers
Comment: C: MicroRNA-target interactions databases
... Dear Kevin, Many thanks for the wonderful answers. As you rightly said there is no "right" or "wrong" way of doing this. I'm new in bioinformatics and R, So I did it all manually, there were few miRNAs (30) and made a merge using the venn diagram. So I import to cytoscape and construction my networ ...
written 7 days ago by Joe Kherery30
6
votes
2
answers
152
views
6 follow
2
answers
MicroRNA-target interactions databases
... Hello everyone, I have a list of 30 microRNAs and I want to build a network of interaction with the targets. Well, I'm thinking about use these databases: 1. [TargetScan Release 7.2][1] 2. [mirTarBase v6.0][2] 3. [enter link description here][3] 4. [microT-CDS 5][4] 5. [miRWalk 3][5] And as a c ...
interaction microrna target written 7 days ago by Joe Kherery30 • updated 6 days ago by Björn20
4
votes
1
answer
123
views
1
answer
Differences between lfc=log2(1.5) and lcf=1.5
... Dears, What is the difference between **lfc=log2(1.5)** and **lcf=1.5** ? topTable <- topTable(fit, coef=1, number=Inf, adjust.method="BH", **lfc=1.5**) Which is the correct one to use and why? Another question is what cut-off to use??? I see many articles using |log2fold change (FC)|≥1 ...
R limma microarray written 11 days ago by Joe Kherery30 • updated 11 days ago by h.mon14k
0
votes
0
answers
84
views
0
answers
Comment: C: Same code for different versions of the same platform
... Dear YaGalbi, OFC I tried this before posting here. And yes it worked, but I'm not sure if there's something missing from the code that is needed in another version of the same platform. ...
written 12 days ago by Joe Kherery30
0
votes
0
answers
84
views
0
answers
Comment: C: Same code for different versions of the same platform
... Dear, Alex Reynolds They did not publish supplementals to compare. ...
written 12 days ago by Joe Kherery30
1
vote
0
answers
84
views
0
answers
Same code for different versions of the same platform
... I would like to use the R code that I wrote to analyze **affymetrix human genome u133 plus 2.0 array** to analyze **Affymetrix Human Genome U219** I would like to know if I can use the same code for different versions of the same platform; library(simpleaffy) celfiles <- read.affy(covd ...
R microarray written 12 days ago by Joe Kherery30
0
votes
0
answers
103
views
0
answers
Comment: C: Functional enrichment of pathways
... Dear Jean-Karim Heriche, I was a bit confused now, I can not remove LOC, LINC and MIR from my list? to make functional enrichment? Since they do not have "GO functions". And keeping them can cause some canonical pathways not to have a significant p-value. ...
written 12 days ago by Joe Kherery30
0
votes
0
answers
103
views
0
answers
Comment: C: Functional enrichment of pathways
... Dear russhh, I only use R. ...
written 13 days ago by Joe Kherery30
0
votes
0
answers
103
views
0
answers
Comment: C: Functional enrichment of pathways
... I use [MSigDB][1] or [enrich][2] via web, sometimes I use panther db too. Can you give me an example of how to filter my list of genes? [1]: http://software.broadinstitute.org/gsea/msigdb/annotate.jsp [2]: http://amp.pharm.mssm.edu/Enrichr/ ...
written 13 days ago by Joe Kherery30

Latest awards to Joe Kherery

Supporter 7 days ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 835 users visited in the last hour