User: Lluís R.

gravatar for Lluís R.
Lluís R.550
Reputation:
550
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
19 hours ago
Joined:
3 years, 10 months 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 • 134 results • page 1 of 14 • next >
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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 9 days ago by Lluís R.550
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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 10 days ago by Lluís R.550
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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 10 days ago by Lluís R.550
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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 21 days ago by Lluís R.550
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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 11 weeks ago by Lluís R.550
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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 11 weeks ago by Lluís R.550
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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 11 weeks ago by Lluís R.550
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Comment: C: Problem with topGO: GO term enrichment analysis
... Yes, not you seem to have created the object correctly. Now you can use it to test the enrichment with runTest... ...
written 3 months ago by Lluís R.550
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Comment: C: WGCNA module colors not identical to further analysis?
... I can't see the images, but that could be due to a misplacement of the names of the modules in either of the pictures ...
written 3 months ago by Lluís R.550
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Comment: C: Using not significant differentially expressed genes
... I was aware of the network point of view, but you brought a nice paper, it points software (and thus new methodology) I hadn't heard before. ...
written 3 months ago by Lluís R.550

Latest awards to Lluís R.

Scholar 11 weeks ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 7 months ago, created 100 posts.
Voter 16 months ago, voted more than 100 times.
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Supporter 3.6 years ago, voted at least 25 times.
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

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