User: Lluís R.

gravatar for Lluís R.
Lluís R.890
Reputation:
890
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
2 weeks ago
Joined:
6 years, 2 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 • 175 results • page 1 of 18 • next >
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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 6 weeks ago by Lluís R.890
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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 3 months ago by Lluís R.890
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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 3 months ago by Lluís R.890
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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 4 months ago by Lluís R.890
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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 4 months ago by Lluís R.890
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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 4 months ago by Lluís R.890
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High fold change values
... I am studying some RNA-seq data with `edgeR` and `limma`. The data was obtained from 59 samples using Illumina HiSeq 2500 and analyzing following the workflow [RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR ][1]. The data is quite complex with 4 different factors interacting betwee ...
rna-seq written 4 months ago by Lluís R.890
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Comment: C: Comparing lists of GOs (not genes)
... How do you define enrichment of clusters of grouped GO IDs? The higher they are similar between them the earlier your clusters will merge ...
written 4 months ago by Lluís R.890
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Answer: A: Comparing lists of GOs (not genes)
... You can use GOSemSim to compare list of GO. It compares them based on semantic similarity of GO terms. ...
written 4 months ago by Lluís R.890
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Comment: C: How To Merge Two Fastq.Gz Files?
... Probably the compression found more patterns when more data was added, thus it could reduce more information. ...
written 6 months ago by Lluís R.890

Latest awards to Lluís R.

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Popular Question 6 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 9 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 10 months ago, created a question with more than 1,000 views. For Installation Of Rnaspace
Scholar 11 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 11 months ago, created a question with more than 1,000 views. For Downloable stats of Bioconductor
Good Answer 15 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 15 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 19 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 19 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Scholar 2.3 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar 2.6 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 2.9 years ago, created 100 posts.
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Popular Question 4.4 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 4.6 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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