User: enricoferrero

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enricoferrero570
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570
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Switzerland
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4 months, 2 weeks ago
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6 years, 1 month ago
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Posts by enricoferrero

<prev • 132 results • page 1 of 14 • next >
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Comment: C: Using RUVSeq RUVs() to perform batch correction using technical replicates
... Thanks both. The two groups have indeed not escaped my attention. There are several other variables in the experiment, both biological and technical, that can affect the PCs (e.g.: treatment, gender). I was planning to first account for the known batch effect using the technical replicates and then ...
written 6 months ago by enricoferrero570
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Comment: C: RNA-seq batch correction using technical replicates profiled across batches
... Awesome, thanks Gordon. I will do as you suggest and report back if I run into problems. ...
written 6 months ago by enricoferrero570
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Comment: C: RNA-seq batch correction using technical replicates profiled across batches
... Thanks Gordon. Please correct me if I'm wrong, but I think a potential problem with this approach is that batch is perfectly confounded with condition so it would not be possible to fit a model of the kind `~ batch + condition`. This is why I would like to use the technical replicates profiled acr ...
written 6 months ago by enricoferrero570
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RNA-seq batch correction using technical replicates profiled across batches
... Hello, I have the following (certainly not ideal) RNA-seq experimental design: - Batch 1 contains 40 samples with condition A + 12 samples with condition B - Batch 2 contains 40 samples with condition C + the same 12 samples with condition B So, the 12 samples with condition B are technical repli ...
limma edger sva deseq2 ruvseq written 6 months ago by enricoferrero570 • updated 6 months ago by Gordon Smyth38k
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Comment: C: DESeq2 w. pathway/network info as a prior knowledge
... Perhaps GSVA is what you’re looking for? It’s a Bioconductor package that shifts the differential expression analysis from genes to gene sets (e.g.: pathways). ...
written 6 months ago by enricoferrero570
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Using RUVSeq RUVs() to perform batch correction using technical replicates
... Ciao Davide, I would be very interested in using RUVSeq::RUVs() as it appears to be the only published and packaged method for correcting batch effects using technical replicates profiled across batches. However, I must be doing something wrong because I can't get it to work. I have a non-ideal e ...
deseq2 ruvseq ruvs written 6 months ago by enricoferrero570 • updated 6 months ago by Gordon Smyth38k
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Comment: C: [limma] Define contrasts for model with covariates
... Thanks Gordon!  Can you please explain why that's the case? I.e.: why only the first categorical variable in the formula gets both levels as coefficients? ...
written 14 months ago by enricoferrero570
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[limma] Define contrasts for model with covariates
... I'm having a hard time understanding how to pull out the relevant contrasts when using a model with covariates in limma. Let's say I have the following gene expression matrix and experimental variables: library(limma) set.seed(16) mat <- matrix(rnorm(600), 100, 6) age <- c(45, 55, 47, 56, ...
limma model.matrix makecontrasts written 14 months ago by enricoferrero570 • updated 14 months ago by Gordon Smyth38k
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Comment: C: Invitation to submit articles to the Bioconductor gateway on F1000Research
... I have a cross-package workflow which was approved by referees a few weeks ago: https://f1000research.com/articles/7-121/v2 I would love for it to be part of BioC 2018 - is that possible even if it was published before the call? ...
written 16 months ago by enricoferrero570
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Comment: C: Gviz IdeogramTrack fails with Error: failed to load HTTP resource
... This might be related to https://support.bioconductor.org/p/105322/ though the error message appears to be different. ...
written 18 months ago by enricoferrero570

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Great Question 8 months ago, created a question with more than 5,000 views. For biomaRt proxy issues
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Popular Question 8 months ago, created a question with more than 1,000 views. For BS-seq differential methylation analysis using continuous variable
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Great Question 15 months ago, created a question with more than 5,000 views. For [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
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Great Question 2.3 years ago, created a question with more than 5,000 views. For [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For biomaRt proxy issues
Popular Question 2.3 years ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
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Popular Question 3.3 years ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How to properly sort GRanges?
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