User: Lluís R.

gravatar for Lluís R.
Lluís R.690
Reputation:
690
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
1 day, 13 hours ago
Joined:
4 years, 5 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 • 154 results • page 1 of 16 • next >
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Comment: C: Using of WGCNA to identify modules in Normal/Tumor tissues
... If you are going right or not might be better addressed by your supervisor. But it seems reasonable to me ...
written 5 days ago by Lluís R.690
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Comment: C: Using of WGCNA to identify modules in Normal/Tumor tissues
... 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 9 days ago by Lluís R.690
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Comment: C: Module- Triat relationship in WGCNA
... 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 days ago by Lluís R.690
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Answer: A: Module- Triat relationship in WGCNA
... 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 days ago by Lluís R.690
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Comment: C: Why different tSNE plot with Seurat and Monocle if they'r using the same R packa
... 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 4 weeks ago by Lluís R.690
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Comment: C: Consensus WGCNA: differentially connected genes
... 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 4 weeks ago by Lluís R.690
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Comment: C: Consensus WGCNA: differentially connected genes
... 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 5 weeks ago by Lluís R.690
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Comment: C: WGCNA with "interlinked" experimental conditions as traits
... I haven't work with LC-MS data or tools so I can't recommend a package for this kind of data, but that one you linked seems a good one. Search the literature and papers that cite it to see if it fits your purpose (after you have read the methodology of the tool). However it is different to test di ...
written 10 weeks ago by Lluís R.690
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Comment: C: WGCNA with "interlinked" experimental conditions as traits
... In some context it seems that it should be enough to find some pattern that is common between conditions. If you want to find soft relationships between genes you need to have highly similar samples and that depends on the effect size of the changes of each condition, but with so many different cond ...
written 10 weeks ago by Lluís R.690
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Answer: A: WGCNA with "interlinked" experimental conditions as traits
... You seem to have very low number of samples per conditions which makes this type of analysis unsuitable for you (if there are high differences by condition), It is recommended to use at least 20 samples for analysis which would mean mixing different conditions, thus making the groups of genes correl ...
written 11 weeks ago by Lluís R.690

Latest awards to Lluís R.

Popular Question 5 months ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 5 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Scholar 7 months ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar 10 months ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 15 months ago, created 100 posts.
Voter 2.0 years ago, voted more than 100 times.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
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