User: Lluís R.

gravatar for Lluís R.
Lluís R.990
Reputation:
990
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
10 hours ago
Joined:
7 years 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 • 184 results • page 1 of 19 • next >
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Comment: C: Running GSVA using open source RNA seq data
... Could you post the errors or messages you get ? "Having issues making/getting" doesn't help much to identify the possible source of confusion/error ...
written 5 weeks ago by Lluís R.990
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Comment: C: Weird volcano plot
... Not sure what do you mean by "merging multiple RNAseq" but have you considered and checked if there is any batch effect? Do you have some samples shared on those datasets or at least some knowledge of a gene that should remain more or less constant? ...
written 12 weeks ago by Lluís R.990
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Answer: A: key lookup changes with AnnotationDbi version
... You are using different Bioconductor versions between computers, which affect the underlying data for hgu219.db. For instance the hgu219.db version on computer 2 is newer than the AnnotationDbi version, which might be one of the reason for this, as hgu219.db uses data and methods provided by Annotat ...
written 4 months ago by Lluís R.990
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Comment: C: key lookup changes with AnnotationDbi version
... Can you provide the version of R, Bioconductor, hgu219.db and AnnotationDbi packages you are using on each computer/platform? ...
written 4 months ago by Lluís R.990
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Answer: A: Things you wish you knew when entering the bioinformatics field
... One thing is missing is to **check** and **double check** the **data**. If you make any assumption check them! - Order of files: check them, it might be alphabetically ordered or numerically. - Database entries: check there aren't any mistakes/typos, you don't want to discover this 1 year later o ...
written 5 months ago by Lluís R.990
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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 7 months ago by Lluís R.990
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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 months ago by Lluís R.990
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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 months ago by Lluís R.990
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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 9 months ago by Lluís R.990
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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 12 months ago by Lluís R.990

Latest awards to Lluís R.

Guru 5 months ago, received more than 100 upvotes.
Scholar 5 months ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Teacher 5 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
Popular Question 10 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Popular Question 17 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 20 months ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Popular Question 21 months ago, created a question with more than 1,000 views. For Installation Of Rnaspace
Scholar 22 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 22 months ago, created a question with more than 1,000 views. For Downloable stats of Bioconductor
Good Answer 2.1 years 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 2.2 years 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 2.5 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
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?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Google Summer Of Code 2014 Gsoc 2014
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Scholar 3.2 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar 3.5 years ago, created an answer that has been accepted. For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 3.8 years ago, created 100 posts.
Voter 4.6 years ago, voted more than 100 times.
Popular Question 5.3 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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