User: gil.hornung

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Posts by gil.hornung

<prev • 20 results • page 1 of 2 • next >
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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 5 weeks 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 5 weeks ago by gil.hornung0 • updated 5 weeks ago by Aaron Lun23k
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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 14 months ago by gil.hornung0 • updated 14 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 14 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 18 months 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 18 months ago by gil.hornung0 • updated 18 months ago by Gordon Smyth37k
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Comment: C: Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (
... Thanks Aaron! ...
written 20 months 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 20 months ago by gil.hornung0 • updated 20 months ago by Aaron Lun23k
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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 2.9 years ago by gil.hornung0
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Comment: C: "Over-correction" in the size-factors of the DESeq2 package
... Thank you, Michael. I learned from this discussion. Indeed, the experiment was very noisy with large variation in number of reads. I'm just trying to salvage what I can. And, ofcourse, I will treat the results with a cup of salt. ...
written 3.1 years ago by gil.hornung0

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Popular Question 2.6 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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