User: Lluís R.
Lluís R. • 710
- Reputation:
- 710
- Status:
- Trusted
- Location:
- Spain, Barcelona
- Website:
- http://b101nfo.blogspo...
- Twitter:
- Lluis_Rev
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 minutes ago
- Joined:
- 4 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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Comment:
C: what next after DEGs?
... That depends on your "biological" question and your data. What question do you want to answer? ...
written 1 day ago by
Lluís R. • 710
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... Yes, it is the basic information of the updates of Bioconductor packages. You can find it explained in [Annotation Packages][1]:
> Annotation packages contain lightly or non-curated data from a public source and are updated with each Bioconductor release (every 6 months).
I'll add it in the or ...
written 9 days ago by
Lluís R. • 710
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... Then you need to correct the modgenes variable to the names you want (`nodeNames = rownames(modTOM)[top]`). ...
written 20 days ago by
Lluís R. • 710
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... If you are going right or not might be better addressed by your supervisor. But it seems reasonable to me ...
written 9 weeks ago by
Lluís R. • 710
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... The way that it is described in the tutorials of WGCNA, yes tumor 1 otherwise 0, but you could also have another variable that is stage, and that would be 0 no tumor, 1 small, 2 bigger, 3 metastasis or whatever. ...
written 10 weeks ago by
Lluís R. • 710
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... Well I don't know anything from this paper beyond what it is described, but looking for the Figure 4 a. it seems like they made the correlation between the condition and the eigengene. If it is accurate or not is another thing... You can do as them, but note that they have more than 4 samples for ea ...
written 10 weeks ago by
Lluís R. • 710
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... Your conditions seems like blocking factor. In the WGCNA it is recommended to make the correlation between the eigenvalue of the module with the phenotype variables. I would recommend however to do the correlation between the eigenvalue of the module with the eigenvalue of your condition.
However, ...
written 10 weeks ago by
Lluís R. • 710
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... Each time you run tSNE you'll get different results. I think you should be able to see this if you do another plot with Seurat and Monocle, you should see that it would change (unless they keep the same seed and random numbers). Also are you sure it is the same data? The first one is painted with tw ...
written 3 months ago by
Lluís R. • 710
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... You could then use DiffCoExp or DiffCoEx (not the same tools) that depend on WGCNA.
No, I was referring to the 2.b.5 section. ...
written 3 months ago by
Lluís R. • 710
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... How do you define the differentially connected genes? Genes that apear in the preserved consensus modules in both datasets? Or genes that change their connectivity and direction in each dataset?.
You can merge the clusters (now I don't remember in which tutorial is this explained, but there is one ...
written 3 months ago by
Lluís R. • 710
Latest awards to Lluís R.
Scholar
16 days ago,
created an answer that has been accepted.
For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Popular Question
16 days ago,
created a question with more than 1,000 views.
For Google Summer Of Code 2014 Gsoc 2014
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Google Summer Of Code 2014 Gsoc 2014
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: StackExchange/Area51 bioinformatics is back
Scholar
9 months ago,
created an answer that has been accepted.
For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar
12 months ago,
created an answer that has been accepted.
For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator
16 months ago,
created a comment with at least 3 up-votes.
For C: StackExchange/Area51 bioinformatics is back
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: StackExchange/Area51 bioinformatics is back
Centurion
17 months ago,
created 100 posts.
Voter
2.2 years ago,
voted more than 100 times.
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Supporter
4.4 years ago,
voted at least 25 times.
Autobiographer
4.4 years ago,
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