User: gil.hornung

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Posts by gil.hornung

<prev • 21 results • page 1 of 3 • next >
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Answer: A: EdgeR RNAseq -- best way to deal with random effects
... 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
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Comment: C: limma with paired samples and a continuous variable
... 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
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limma with paired samples and a continuous variable
... 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 | |---------|-----------|-------| ...
limma written 8 months ago by gil.hornung0 • updated 8 months ago by Aaron Lun25k
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Why does the Glimma package require R >= 3.4.0 ?
... 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 ...
glimma written 21 months ago by gil.hornung0 • updated 21 months ago by Shian Su20
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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
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Comment: C: Strong upwards correlation between log fold change and average log expression in
... 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
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Strong upwards correlation between log fold change and average log expression in MD plot of Limma
... 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 ...
proteomics limma written 2.1 years ago by gil.hornung0 • updated 2.1 years ago by Gordon Smyth39k
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Comment: C: Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (
... Thanks Aaron! ...
written 2.2 years ago by gil.hornung0
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Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
... 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 ...
chip-seq csaw histone chip-seq written 2.2 years ago by gil.hornung0 • updated 2.2 years ago by Aaron Lun25k
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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

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