User: Lluís R.

gravatar for Lluís R.
Lluís R.500
Reputation:
500
Status:
Trusted
Location:
Spain, Barcelona
Website:
http://b101nfo.blogspo...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
1 day, 20 hours ago
Joined:
3 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 • 122 results • page 1 of 13 • next >
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Comment: C: How To Change An Expertise In Bioinformatics
... Strange that because blogging is "cheap" it doesn't worth it. ...
written 17 days ago by Lluís R.500
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Comment: C: How can I increase the sensitivity of WGCNA modules?
... I could only find the minimum in minModuleSize, I might have confused with another option. Sorry. ...
written 19 days ago by Lluís R.500
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Comment: C: How can I increase the sensitivity of WGCNA modules?
... You can specify a max number of genes per module to avoid big modules. You could also apply the same mergeCutHeight algorithm to a given module. ...
written 20 days ago by Lluís R.500
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Comment: C: Plot of up and down regulated metabolic pathways in this way
... Yes, n and m are simple fractions. The scatterplot will only plot the points for each pathway but then you can add the dashed lines with abline. Check the help of the functions about how do they work. ...
written 4 weeks ago by Lluís R.500
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Comment: C: verboseScatterplot generate cor and pvalue not same as moduleTraitCor
... I don't understand the question, what is not the same, could you post the numeric differences between them (and where do you calculate each?) ...
written 4 weeks ago by Lluís R.500
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Comment: C: compare gene networks
... Read the tutorials at the [webpage][1], there is one that compares modules robustness even across networks (I don't recall now which one). [1]: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/ ...
written 4 weeks ago by Lluís R.500
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Answer: A: goodSamplesGenesMS non-numeric variable in data frame multiExpr
... I guess (it would be better if you provide information about your multiExpr) that you have characters instead of numbers in one of the matrices. Check that with `sapply(multiExpr, function(x){all(sapply(x$data, is.numeric))})` ...
written 4 weeks ago by Lluís R.500
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Answer: A: Plot of up and down regulated metabolic pathways in this way
... The relevant section of the methods is "Identification of metabolic pathways with significant expression changes." and "Statistical significance of the observed metabolic pathway expression patterns.". - You need to calculate if a pathway in up or down regulated for each of sample (tumor, conditi ...
written 4 weeks ago by Lluís R.500
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Comment: C: GSEA produces too few enriched sets
... Why is that wrong? What reasons do you have to expect having more gene sets enriched in your experiment? What I don't understand is how you used KEGG metabolic pathways of a relative organism "to classify DEGs and check pathways enrichment", first you classify DEGs based on your knowledge, and then ...
written 4 weeks ago by Lluís R.500
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Comment: C: WGCNA export Network To Cytoscape without trait data, error "Cannot determine no
... So your nodeNames are NULL. Probably, but ask your supervisor or a college. ...
written 5 weeks ago by Lluís R.500

Latest awards to Lluís R.

Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: StackExchange/Area51 bioinformatics is back
Centurion 3 months ago, created 100 posts.
Voter 12 months ago, voted more than 100 times.
Popular Question 20 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 Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
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