User: Lluís Revilla Sancho

Reputation:
430
Status:
Trusted
Location:
European Union
Website:
https://b101nfo.blogsp...
Twitter:
Lluis_Rev
Last seen:
3 hours ago
Joined:
3 years, 10 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís Revilla Sancho

<prev • 207 results • page 1 of 21 • next >
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Error installing graphite
... I have some problems installing graphite since the new release of Bioconductor. Initially I had trouble allocating a vector of certain size. However, on the last try I got a new error, related to graphite.ts before getting the same error message: > BiocManager::install("graphite") Bioconductor ve ...
graphite written 1 day ago by Lluís Revilla Sancho430
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Answer: A: Can not install packages
... To install packages from Bioconductor you need the BiocManager package: install.packages("BiocManager") BiocManager::install(c("ballgown", "genefilter")) However, to get the latest packages from Bioconductor you'll need R version 3.5 not the R version 3.4.4 you are using. ...
written 7 days ago by Lluís Revilla Sancho430
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Comment: C: Using Kendall's Tau rank correlation coefficient for creating WGCNA network
... Depending on how big is your dataset you should follow the manual strategy. This will allow you to create the adjacency matrix for looking for the modules. ...
written 8 days ago by Lluís Revilla Sancho430
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Answer: A: compute similarities of GOTerms with GOSim in non-human species
... To build the IC you need to tho this: library(GOSemSim) GOMF <- godata('org.At.tair.db', ont="MF") And use this GOMF object to calculate the similarity between molecular function terms of Arabidopsis thaliana. You can find this information under Supported organisms' section of the vignette. ...
written 19 days ago by Lluís Revilla Sancho430
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Comment: C: problem for finding soft thresholding in WGCNA algorithm
... You need to read the documentation and the articles surrounding WGCNA, but all of them are provided by pickSoftThreshold: the mean,k, median.k... For a signed network you need to do the same justify your decisions. I won't make the decision for you. ...
written 29 days ago by Lluís Revilla Sancho430
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Comment: C: problem for finding soft thresholding in WGCNA algorithm
... I would use 5 as power, because the SFT.R.sq but also the other metrics are better for 5 rather than for 6. ...
written 29 days ago by Lluís Revilla Sancho430
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Comment: C: problem for finding soft thresholding in WGCNA algorithm
... Both of them are ok, after all there is not any guarantee that the biological systems are scale free. However, you will need to explain why you choose 0.8. It might be enough saying that you couldn't reach better scale-free indicators with higher power. ...
written 29 days ago by Lluís Revilla Sancho430
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Comment: C: problem for finding soft thresholding in WGCNA algorithm
... All those 50 samples are from the same type of cancer? If not the lack of power might be due to this. ...
written 4 weeks ago by Lluís Revilla Sancho430
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Comment: C: problem for finding soft thresholding in WGCNA algorithm
... The problem with the plot is that the values barely reach the 0.8 threshold, so when you plot the line at 0.9 it is out of the y axis of the plot. Why you don't reach the 0.9 I can't say, probably it means that the dataset is not homogeneous. Maybe there is too much variability and too few samples ...
written 4 weeks ago by Lluís Revilla Sancho430
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Comment: C: WGCNA tree creation
... What problems did you found? What/How many clinical variables do  you have? ...
written 7 weeks ago by Lluís Revilla Sancho430

Latest awards to Lluís Revilla Sancho

Popular Question 6 weeks 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 6 weeks 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 5 months ago, created an answer with at least 3 up-votes. For A: Where can I use the VSN source code in C++?
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 6 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 16 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 16 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 16 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Scholar 16 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 16 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
Voter 17 months ago, voted more than 100 times.
Centurion 19 months ago, created 100 posts.
Scholar 3.8 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 3.8 years ago, voted at least 25 times.

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