User: Joe Kherery

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Joe Kherery30
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10 months, 2 weeks ago
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Posts by Joe Kherery

<prev • 29 results • page 1 of 3 • next >
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Comment: C: How to predict the cellular origin of expression of a gene in a blood sample?
... Thank you very much, it seems like this is what I really need. ...
written 4 months ago by Joe Kherery30
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How to predict the cellular origin of expression of a gene in a blood sample?
... Hello ladies and gentlemen, I have a set of differentially expressed blood-derived genes from patients against healthy patients. So I wondered if there was a way to predict which cell type would most likely be expressing that gene? Example: monotics, eosinophils ... Best, ...
in silico microarray written 4 months ago by Joe Kherery30 • updated 4 months ago by igor6.8k
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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 5 months ago by Joe Kherery30
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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 5 months ago by Joe Kherery30
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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 5 months ago by Joe Kherery30 • updated 5 months ago by Björn30
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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 5 months ago by Joe Kherery30 • updated 5 months ago by h.mon20k
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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 5 months ago by Joe Kherery30
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Comment: C: Same code for different versions of the same platform
... Dear, Alex Reynolds They did not publish supplementals to compare. ...
written 5 months ago by Joe Kherery30
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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 5 months ago by Joe Kherery30
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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 5 months ago by Joe Kherery30

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