The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

User: enricoferrero

gravatar for enricoferrero
enricoferrero570
Reputation:
570
Status:
Trusted
Location:
Switzerland
Last seen:
6 hours ago
Joined:
5 years, 7 months ago
Email:
e**************@gmail.com

Posts by enricoferrero

<prev • 132 results • page 1 of 14 • next >
0
votes
1
answer
70
views
1
answers
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 3 days ago by enricoferrero570
0
votes
1
answer
96
views
1
answers
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 4 days ago by enricoferrero570
0
votes
1
answer
96
views
1
answers
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 4 days ago by enricoferrero570
4
votes
1
answer
96
views
1
answer
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 5 days ago by enricoferrero570 • updated 4 days ago by Gordon Smyth36k
0
votes
1
answer
264
views
1
answers
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 5 days ago by enricoferrero570
1
vote
1
answer
70
views
1
answer
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 days ago by enricoferrero570 • updated 3 days ago by Gordon Smyth36k
0
votes
1
answer
288
views
1
answers
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 8 months ago by enricoferrero570
4
votes
1
answer
288
views
1
answer
[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 8 months ago by enricoferrero570 • updated 8 months ago by Gordon Smyth36k
0
votes
0
answers
1.3k
views
0
answers
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 10 months ago by enricoferrero570
0
votes
0
answers
302
views
0
answers
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 12 months ago by enricoferrero570

Latest awards to enricoferrero

Great Question 8 months ago, created a question with more than 5,000 views. For [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
Popular Question 8 months ago, created a question with more than 1,000 views. For Linkage disequilibrium with 1000 Genomes/HapMap
Popular Question 8 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
Popular Question 21 months ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Popular Question 21 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
Popular Question 21 months ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
Scholar 21 months ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Popular Question 21 months ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Great Question 21 months ago, created a question with more than 5,000 views. For How to properly sort GRanges?
Great Question 21 months ago, created a question with more than 5,000 views. For [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
Popular Question 22 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
Student 22 months ago, asked a question with at least 3 up-votes. For Can't upgrade to Bioconductor 3.3?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For biomaRt proxy issues
Scholar 2.8 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Centurion 2.8 years ago, created 100 posts.
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Linkage disequilibrium with 1000 Genomes/HapMap
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Popular Question 2.8 years ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
Scholar 2.8 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For biomaRt no longer works with proxy after upgrade
Popular Question 3.1 years ago, created a question with more than 1,000 views. For biomaRt no longer works with proxy after upgrade
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Scholar 3.2 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Supporter 3.3 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 362 users visited in the last hour