## User: gil.hornung

Reputation:
0
Status:
New User
Last seen:
1 week, 2 days ago
Joined:
3 years, 11 months ago
Email:
g**********@weizmann.ac.il

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

#### Posts by gil.hornung

<prev • 21 results • page 1 of 3 • next >
2
473
views
2
... There is also another package, called dream which enables the use of random effects in RNA-seq data analysis. I haven't used it personally. https://www.biorxiv.org/content/biorxiv/early/2018/10/03/432567.full.pdf https://bioconductor.riken.jp/packages/devel/bioc/vignettes/variancePartition/inst/ ...
written 23 days ago by gil.hornung0
1
172
views
1
... Thank you Aaron for the fast and helpful reply! One question: I thought that the "patients" is more of "random effects" than "fixed effect" (although, to be honest, I never really understood the difference between the two). This is why I though of using duplicateCorrelation and block. What do y ...
written 8 months ago by gil.hornung0
1
172
views
1
... Hi, I have expression data from patients that underwent treatment with a drug, before and after treatment. I also have a measurement of something in their blood, which I call "score". The samples metadata looks something like this: | patient .| treatment. | score | |---------|-----------|-------| ...
written 8 months ago by gil.hornung0 • updated 8 months ago by Aaron Lun25k
1
292
views
1
... Hi,   The Glimma package is great for exploring Differential Expression results, but it requires R version >= 3.4.0  Unfortunately, in my organisation the production pipeline relies on R 3.2.1  If I "hack" the Glimma package and change the Depends line in the DESCRIPTION file to `Depends: R ...
written 21 months ago by gil.hornung0 • updated 21 months ago by Shian Su20
2
1.1k
views
2
Answer: A: Affymetrix Mogene 1 0 ST
... I was also wondering about the normgene->exon and normgene->intron probe types, and after a long search found it in the "Quality Assessment of Exon and Gene Arrays" whitepaper from Affymetrix. This is the current link: https://tools.thermofisher.com/content/sfs/brochures/exon_gene_arrays_qa_ ...
written 21 months ago by gil.hornung0
2
567
views
2
... Thank you Gordon and James for the fast and helpful answers. I used "1+" in my model and it worked fine.   Al the best ,   Gil ...
written 2.1 years ago by gil.hornung0
2
567
views
2
... Hi, I am trying to analyse my proteomics data (intensity based label free quantification) using Limma. When I look at the MD plot after limma fit, I see a strong correlation between log-fold-change and average-log-expression. What could cause this odd behaviour and how can I fix it? Thanks, Gil ...
written 2.1 years ago by gil.hornung0 • updated 2.1 years ago by Gordon Smyth39k
1
458
views
1
... Thanks Aaron! ...
written 2.2 years ago by gil.hornung0
1
458
views
1
... Hi, I am interested in H3K9me2 signal (in S. Pombe), which is abundant on telomeres and centromeres. These regions are notorious for being highly repetitive. I clearly see an effect between treated and control samples in the coverage on telomeres, and I would like to quantify these differences usin ...
written 2.2 years ago by gil.hornung0 • updated 2.2 years ago by Aaron Lun25k
3
7.0k
views
3
Comment: C: pre-ranked GSEA within R?
... A faster GSEA is great. Did you implement it in the stable release? I'm using version 1.10.2 and it is still slow. ...
written 3.4 years ago by gil.hornung0

#### Latest awards to gil.hornung

Popular Question 8 months ago, created a question with more than 1,000 views. For "Over-correction" in the size-factors of the DESeq2 package
Popular Question 13 months ago, created a question with more than 1,000 views. For "Over-correction" in the size-factors of the DESeq2 package
Popular Question 3.2 years ago, created a question with more than 1,000 views. For "Over-correction" in the size-factors of the DESeq2 package

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.