User: Lluís Revilla Sancho

Reputation:
530
Status:
Trusted
Location:
European Union
Website:
https://b101nfo.blogsp...
Twitter:
Lluis_Rev
Scholar ID:
Google Scholar Page
Last seen:
17 hours ago
Joined:
4 years, 10 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís Revilla Sancho

<prev • 245 results • page 1 of 25 • next >
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Answer: C: Why package "BiocLite" is not available (for R version 3.6.1)
... The biocLite script was deprecated as it could induce to errors and installing malicious code. If you are using R 3.6.1 you don't need it any more, with BiocManager you can do the same you previously did with biocLite and BiocInstaller. For completeness, you see that BiocInstaller was removed on Bi ...
written 5 days ago by Lluís Revilla Sancho530
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Downloading a private GEO with GEOquery
... I am trying to access some unpublished data from GEO for which I know the GSE number and the access token. I would like to download it. However, I couldn't download it using `getGEO`. I tried both using just the GSE and with a modified version with the token at the end ```r gse <- getGEO("GSE01 ...
geoquery written 6 weeks ago by Lluís Revilla Sancho530 • updated 6 weeks ago by Sean Davis21k
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Comment: C: GOplot error - Gene Ontology plot generation errors
... What are those perl scripts you mention on the question doing? Could you show the R code being called? ...
written 7 weeks ago by Lluís Revilla Sancho530
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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 3 months ago by Lluís Revilla Sancho530
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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 3 months ago by Lluís Revilla Sancho530
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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 3 months ago by Lluís Revilla Sancho530
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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 3 months ago by Lluís Revilla Sancho530
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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 3 months ago by Lluís Revilla Sancho530
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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 4 months ago by Lluís Revilla Sancho530
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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 4 months ago by Lluís Revilla Sancho530

Latest awards to Lluís Revilla Sancho

Popular Question 10 months ago, created a question with more than 1,000 views. For Installing arrayQualityMetrics: ERROR: lazy loading failed
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
Popular Question 13 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 13 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
Teacher 17 months 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
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Where can I use the VSN source code in C++?
Teacher 18 months 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 2.4 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 2.4 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 2.4 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 2.4 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 2.4 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 4.8 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?

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