User: 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:
- 14 hours ago
- Joined:
- 3 years, 7 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.
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... 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 14 days ago by
Lluís R. • 550
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... 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 14 days ago by
Lluís R. • 550
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... Yes! WGCNA creates groups of genes working coordinated. But you'll need more than 20 samples per condition. ...
written 14 days ago by
Lluís R. • 550
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... Yes, not you seem to have created the object correctly. Now you can use it to test the enrichment with runTest... ...
written 4 weeks ago by
Lluís R. • 550
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... 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 4 weeks ago by
Lluís R. • 550
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... 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 5 weeks ago by
Lluís R. • 550
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... Thanks I am aware of SPIA (although I have never used it), all GSEA methods use both DE and non DE genes. Thanks ...
written 5 weeks ago by
Lluís R. • 550
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... The number of counts don't decide if a gene would clustered into one module or another. To set a gene in a module or in another what it is important (for WGCNA) is if the correlation between the genes is high.
To calculate the cluster preservation there is a function (modulePreservation), as well ...
written 7 weeks ago by
Lluís R. • 550
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... Strange that because blogging is "cheap" it doesn't worth it. ...
written 10 weeks ago by
Lluís R. • 550
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... I could only find the minimum in minModuleSize, I might have confused with another option. Sorry. ...
written 11 weeks ago by
Lluís R. • 550
Latest awards to Lluís R.
Scholar
14 days ago,
created an answer that has been accepted.
For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator
4 months ago,
created a comment with at least 3 up-votes.
For C: StackExchange/Area51 bioinformatics is back
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: StackExchange/Area51 bioinformatics is back
Centurion
5 months ago,
created 100 posts.
Voter
14 months ago,
voted more than 100 times.
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
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?
Supporter
3.4 years ago,
voted at least 25 times.
Autobiographer
3.4 years ago,
has more than 80 characters in the information field of the user's profile.
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