User: Lluís Revilla Sancho

Reputation:
500
Status:
Trusted
Location:
European Union
Website:
https://b101nfo.blogsp...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
17 minutes ago
Joined:
4 years, 8 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís Revilla Sancho

<prev • 242 results • page 1 of 25 • next >
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Comment: C: Diagnosing topGo issue - single enriched gene per enriched GO term
... Welcome to the site. Could you please format your results better, I am not sure I understand the output. Also if you could share the function call and show some of your input data it would be easier to understand where the problem might be ...
written 6 weeks ago by Lluís Revilla Sancho500
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Comment: C: GO enrichment for non-model plant species
... I think that you can convert it to a list, or it is already accepted, but check the vignette and the manuals ...
written 6 weeks ago by Lluís Revilla Sancho500
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Comment: C: GO enrichment for non-model plant species
... How did you create the gmt file? Did you try to create a GeneSetCollection for clusterProfiler (this way you wouldn't need to create a gmt file)? ...
written 6 weeks ago by Lluís Revilla Sancho500
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Answer: A: Choosing Gene ontology package
... You can use topGO package to compare the enrichment of these methods, or compare the similarity of the clusters using GOSemSim ...
written 6 weeks ago by Lluís Revilla Sancho500
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Comment: C: writing gse series matrix data into a csv file
... Which version of Bioconductor (and R) are you using? It doesn't seem the latest version. I didn't understand the description of the file output, but have you looked at `write.csv`? ...
written 7 weeks ago by Lluís Revilla Sancho500
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Comment: C: Meaning of NA in geneSim result using GOSemSim
... The data seems different the dag contains 4212625 vertex, while the mmGO data just 163654, probably because the dag annotates all the genes to all the parent GO terms. But mainly the differences come from having different source of data ...
written 8 weeks ago by Lluís Revilla Sancho500
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Comment: C: Meaning of NA in geneSim result using GOSemSim
... Unless there is some difference (bug or not) on the implementation of the algorithm the most probable difference is the source of data. Without knowing which functions and data you used I cannot see were come the differences. However, it can be that GOSemSim filtered the annotations with annotation ...
written 8 weeks ago by Lluís Revilla Sancho500
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Answer: A: Installing arrayQualityMetrics: ERROR: lazy loading failed
... As it seems that this question is getting lots of views I think (I'm not sure now) that I followed the recommendation of Martin of removing the locked files. ...
written 9 weeks ago by Lluís Revilla Sancho500
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Answer: A: Using GoSemSim with other Ontologies
... In principle it should, you should prepare the ontolgoy as described on the vignette with `godata`and the semantic similarities would work. However, make sure that the ontology follows the same structure than the gene ontology. ...
written 9 weeks ago by Lluís Revilla Sancho500
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Comment: C: Discrepancies between topGO output and input
... Could it be that some other genes are annotated to a GO term that implies this "defense response" term? I don't recall now if in this case the number of reported genes would be the ones directly annotated to a term or all that are linked to it. ...
written 10 weeks ago by Lluís Revilla Sancho500

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Popular Question 8 months ago, created a question with more than 1,000 views. For Installing arrayQualityMetrics: ERROR: lazy loading failed
Popular Question 9 months ago, created a question with more than 1,000 views. For Unable to calculate in parallel what can be calculated on a for loop
Popular Question 11 months ago, created a question with more than 1,000 views. For Unable to calculate in parallel what can be calculated on a for loop
Scholar 11 months ago, created an answer that has been accepted. For A: Does anyone need to install an R package which is used by another package as imp
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Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Does anyone need to install an R package which is used by another package as imp
Scholar 2.2 years ago, created an answer that has been accepted. For A: Does anyone need to install an R package which is used by another package as imp
Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Does anyone need to install an R package which is used by another package as imp
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Scholar 4.7 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?

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