User: Lluís R.

gravatar for Lluís R.
Lluís R.910
Reputation:
910
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
1 week, 6 days ago
Joined:
6 years, 6 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 • 179 results • page 1 of 18 • next >
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Comment: C: Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed
... There isn't any problem on the dimensionality of DEG test, as more genes lead to better estimation of the parameters of the genes. How do you do GSEA before having an ordered list? Yes usually GSEA methods do not evaluate if a pathway is up or down-regulated (how would it know? ) ...
written 20 days ago by Lluís R.910
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Answer: C: TopGo corrupts long term names ' https://support.bioconductor.org/p/131412/ '
... Crossposted on Bioconductor: https://support.bioconductor.org/p/131412/ ...
written 9 weeks ago by Lluís R.910
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Comment: C: topGO analysis "MF" term error
... Great that it was easy to solve. No, don't delete it, you might help future reader who has the same problem ...
written 9 weeks ago by Lluís R.910
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Comment: C: topGO analysis "MF" term error
... Which version of R and Bioconductor are you using? Which is the version of org.Rn.eg.db ? I think there was some trouble on the latest release with the GO.db package and they updated it. Check if you need to update, otherwise the code looks good and should work imho. ...
written 10 weeks ago by Lluís R.910
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Comment: C: WGCNA export Network To Cytoscape without trait data, error "Cannot determine no
... No, that's what the original poster used. I limited to copy and correct the error ...
written 5 months ago by Lluís R.910
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Comment: C: functional enichment with custom gene annotation
... You keep using the word network but you don't specify in which format do you have this network. How are the edges and nodes of this network stored? Or these custom network is just a list of co-expressed or a selection of genes? ...
written 8 months ago by Lluís R.910
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Comment: C: functional enichment with custom gene annotation
... You are commenting that you have a list of genes that are networks. How do you define those networks ? And what type of enrichment are you looking for? ...
written 8 months ago by Lluís R.910
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Compare samples that don't have a coefficient on the design matrix
... I have some data that I model with 4 factors, each one have two levels. However, I need to compare some samples based on a fifth factor that is not included on the model: Here I provide an example design matrix: groups <- paste(c("f1A", "f1B", "f1A", "f1A", "f1B", "f1A"), ...
comparisons R linar-model written 8 months ago by Lluís R.910
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Comment: C: High fold change values
... I don't think it is. You can find the boxplot [here](https://i.ibb.co/5rmrFhc/log-CPM.png), also here [after voom](https://i.ibb.co/QPftzCy/voom-boxplot.png) normalization ...
written 8 months ago by Lluís R.910
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Comment: C: High fold change values
... I filtered using `edgeR::filterByExpr`, that is min.count = 10 and min.total.count = 15. But I haven't looked at cpm, I'll look at it. When I mention the 75% of DEG is looking only to the FDR < 0.05. ...
written 8 months ago by Lluís R.910

Latest awards to Lluís R.

Scholar 9 weeks ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Popular Question 3 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
Popular Question 10 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 13 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 14 months ago, created a question with more than 1,000 views. For Installation Of Rnaspace
Scholar 15 months ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Popular Question 15 months ago, created a question with more than 1,000 views. For Downloable stats of Bioconductor
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Difference between GO.db, biomaRt, and org.Hs.eg.db in GO annotations
Appreciated 19 months ago, created a post with more than 5 votes. For A: Difference between GO.db, biomaRt, and org.Hs.eg.db in GO annotations
Scholar 23 months ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Popular Question 23 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
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?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Scholar 2.7 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar 2.9 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 3.3 years ago, created 100 posts.
Voter 4.1 years ago, voted more than 100 times.
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Supporter 6.3 years ago, voted at least 25 times.
Autobiographer 6.3 years ago, has more than 80 characters in the information field of the user's profile.

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