User: Lluís R.

gravatar for Lluís R.
Lluís R.880
Reputation:
880
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
5 years, 10 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 • 174 results • page 1 of 18 • next >
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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 2 days ago by Lluís R.880
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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 5 days ago by Lluís R.880
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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 days ago by Lluís R.880
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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 12 days ago by Lluís R.880
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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 13 days ago by Lluís R.880
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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 13 days ago by Lluís R.880
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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 14 days ago by Lluís R.880
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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 14 days ago by Lluís R.880
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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 10 weeks ago by Lluís R.880
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Answer: A: Downloable stats of Bioconductor
... As this seems to be popular since then there is a [package][1] BiocPkgTools, currently only in github to download and analyse the data [1]: https://seandavi.github.io/BiocPkgTools/articles/BiocPkgTools.html#download-statistics ...
written 7 months ago by Lluís R.880

Latest awards to Lluís R.

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 5 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 6 months ago, created a question with more than 1,000 views. For Installation Of Rnaspace
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
Popular Question 7 months ago, created a question with more than 1,000 views. For Downloable stats of Bioconductor
Good Answer 11 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 11 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 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 Google Summer Of Code 2014 Gsoc 2014
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 22 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Scholar 2.0 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar 2.3 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 2.6 years ago, created 100 posts.
Voter 3.4 years ago, voted more than 100 times.
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Supporter 5.7 years ago, voted at least 25 times.
Autobiographer 5.7 years ago, has more than 80 characters in the information field of the user's profile.

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