User: Lluís Revilla Sancho

Reputation:
400
Status:
Trusted
Location:
European Union
Website:
https://b101nfo.blogsp...
Twitter:
Lluis_Rev
Last seen:
15 hours ago
Joined:
3 years, 9 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís Revilla Sancho

<prev • 203 results • page 2 of 21 • next >
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Comment: C: Segfault error when loading WGCNA
... I would recommend to use the latest R version (and the latest WGCNA version). This seems to be from a problem in the C++ code of WGCNA ...
written 6 weeks ago by Lluís Revilla Sancho400
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Error setting up a sample in OSAT
... I try to use the setup.sample that worked in the examples but I have found an error library("OSAT") pheno <- structure(list(`Sample Name_RNA` = c("001-w000", "001-w014"), IBD = c("CD", "CD")), row.names = 1:2, class = "data.frame") gs <- setup.sample(pheno[1:2, c("Sample Name_RNA", "IBD")], ...
osat written 12 weeks ago by Lluís Revilla Sancho400
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Comment: C: topGO enrichment analysis
... topGO requires a list of genes and the p-values associated with these genes. But you need to create the topGOdata object in order to be able to use the test ...
written 3 months ago by Lluís Revilla Sancho400
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Comment: C: topGO: how to rettrieve (long) GO term description without abbreviating
... I haven't been using topGO for a while, but I think it could output the whole term name, but maybe it is not displayed (or I could be wrong). ...
written 3 months ago by Lluís Revilla Sancho400
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Comment: C: topGO: how to rettrieve (long) GO term description without abbreviating
... Perhaps you can use a workaround looking into the GO.db package for the terms of these ids.   ...
written 3 months ago by Lluís Revilla Sancho400
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Comment: C: pathview: Warning: Download of hsa04110 xml and png files failed!
... This is not the latest version of R nor of Biocondutor, for these reason I would recommend you to upgrade your R and Bioconductor versions and check in the new version if the error persist. ...
written 3 months ago by Lluís Revilla Sancho400
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Answer: A: TopGO ks test using a score different from p-value
... Theoretically yes, you could use it, you would need to change the selectFun argument, and provide a function that selects the desired genes. However, I think you won't be able to do it because, what I recall when I tried, the selectFun hadn't changed (it is x < 0.05) and it didn't select any gen ...
written 3 months ago by Lluís Revilla Sancho400
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Comment: C: pathview: Warning: Download of hsa04110 xml and png files failed!
... Could you please provide the version of the package you use and the R version number ...
written 3 months ago by Lluís Revilla Sancho400
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Comment: C: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... Ok, I'll try it next time. I wasn't sure it was possible to encode this. Mainly the biological unit can be interpreted differently: a biological unit is the type of lesion or the patient or the biopsy; depending on the question it can be either of them. Many thanks for resolving the issue. PS: I di ...
written 3 months ago by Lluís Revilla Sancho400
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Comment: C: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... Could you please provide an example of how to encode the following SummarizedExperiments in the MultiAssayExperiment colData. SE1: | biopsy | patient| lesion | |--------|--------|--------| | 1 | HC | A | SE2: | biopsy | patient| lesion | |--------|--------|--------| | 1 | HC | ...
written 3 months ago by Lluís Revilla Sancho400

Latest awards to Lluís Revilla Sancho

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Where can I use the VSN source code in C++?
Teacher 4 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 5 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 15 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 15 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
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 15 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 15 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Voter 16 months ago, voted more than 100 times.
Centurion 18 months ago, created 100 posts.
Supporter 3.8 years ago, voted at least 25 times.
Scholar 3.8 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?

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