User: Lluís R.

gravatar for Lluís R.
Lluís R.590
Reputation:
590
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
17 hours ago
Joined:
4 years ago
Email:
l************@gmail.com

I am interested nowadays in microarrays, RNA-Seq and genome annotation, GO and pathways. But my goal are to maximize the useful information of each existing experiment. Now I am committing with Bioconductor, you can follow some of my thought in my blog, or in twitter.

Posts by Lluís R.

<prev • 137 results • page 1 of 14 • next >
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Comment: C: Are OTUs an accurate measure of abundance?
... Nice paper, but it uses rarefaction which has been [recently criticized][1] (https://www.ncbi.nlm.nih.gov/pubmed/24699258) [1]: http://dx.plos.org/10.1371/journal.pcbi.1003531 ...
written 5 weeks ago by Lluís R.590
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Answer: A: Difference between GO.db, biomaRt, and org.Hs.eg.db in GO annotations
... GO.db and org.Hs.eg.db are copies of the GO annotations. GO.db is updated every 6 months with each release of Bioconductor. org.Hs.eg.db is also updated at the same time and using GO.db. biomaRt connects to the server where the informations is stored, so it will be the most up to date. If you wan ...
written 10 weeks ago by Lluís R.590
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Comment: C: Comparing DEG result from different experiment
... If they are properly normalized and are the same comparisons on the same biological and experimental background yes. Different methods should agree on the magnitude of the change if not in the value itself, apply common sense. ...
written 12 weeks ago by Lluís R.590
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Comment: C: RNA Seq data for WGCNA
... Sorry but I think I did not understand your comment. Would you mind clarifying why do you say WGCNA will not work? Which metrics for samples and genes are you talking about ? By using gene set enrichment tools I am including gene ontologies. ...
written 3 months ago by Lluís R.590
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Comment: C: RNA Seq data for WGCNA
... First, it doesn't make sense to look for biologically interesting modules and then restrict to those which have a similar change. First work with WGCNA all samples that have the same biological state (don't mix condition A and controls), Then evaluate if those modules are coherent between two condi ...
written 3 months ago by Lluís R.590
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Comment: C: RNA Seq data for WGCNA
... When you say > 1000 * 4 (1000 - genes and 4 - logFC value). Does it mean you have filtered by logFC? You shouldn't do that. See the FAQ of WGCNA. If you have just 4 samples, then the results will be spurious. WGCNA relays on correlations and you can have quite easily a high correlation with j ...
written 3 months ago by Lluís R.590
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Comment: C: Installing R version 3.2.2 on Ubuntu (17.04)
... Also, consider to install the latest version of R (3.4.2 ) ...
written 3 months ago by Lluís R.590
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Comment: C: Examining connectivity of specific genes in WGCNA
... Depend what kind of co-expression relation do you want and how pure is. The better it would be to have enough samples per group otherwise the differences between the groups might hide real connections between genes. 1. Yes. It is not unusual to do so. In fact WGCNA has functions to do so (but I w ...
written 5 months ago by Lluís R.590
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Answer: A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
... Gene Set Enrichment methods are designed precisely for that purpose. Having your list of genes (transcripts ) of interest you can apply these methods to the whole list of genes to observe if there is any difference of this group of genes, for instance, it is more expressed in the disease rather than ...
written 5 months ago by Lluís R.590
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Comment: C: Examining connectivity of specific genes in WGCNA
... Yes! WGCNA creates groups of genes working coordinated. But you'll need more than 20 samples per condition. ...
written 5 months ago by Lluís R.590

Latest awards to Lluís R.

Popular Question 9 days ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 12 days ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Scholar 10 weeks ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar 5 months ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 10 months ago, created 100 posts.
Voter 19 months ago, voted more than 100 times.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Supporter 3.9 years ago, voted at least 25 times.
Autobiographer 3.9 years ago, has more than 80 characters in the information field of the user's profile.

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