User: Lluís R

gravatar for Lluís R
Lluís R310
Reputation:
310
Status:
Trusted
Location:
European Union
Last seen:
an hour ago
Joined:
3 years ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 168 results • page 2 of 17 • next >
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Answer: A: warning: example doesn't exist; while trying to build a package
... If the example is several lines long as it is your case, then you need to use `@examples` as pointed by shepheri. Also make sure that you don't need a space after #' usually I have seen the code with #' (note the space after the '. ...
written 11 weeks ago by Lluís R310
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Comment: C: How to solve "WARNING: Add non-empty \value" with roxygen tags
... I removed the @format tag because what you seemed to describe is what it returns, but if you are describing the structure of the dataset you can use it in addition to @return. Although I am not sure if forcing to have a @return is  strictly followed in the review of packages as it seems more address ...
written 11 weeks ago by Lluís R310
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Answer: A: How to solve "WARNING: Add non-empty \value" with roxygen tags
... The warning tells you need to have the value field in the .Rd files. Using roxygen2 you need to use @return which in the .Rd files is converted into the \value field: #' Features of five human Rel A proteins #' #' List of features from five human NFkappaB proteins downloaded from #' Uniprot on 15 ...
written 11 weeks ago by Lluís R310
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Comment: C: WGCNA - module membership via max kME?
... How many samples do you have? Which is your scale-free topology threshold? What coverage do you have? Are you filtering by low abundance genes or are you filtering them somehow? ...
written 11 weeks ago by Lluís R310
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Answer: A: Setting soft threshold when comparing 2 networks in WGCNA?
... AFAIK, yes, the soft threshold is to find the point where the underlying scale-free topology network structure emerge. It seems that they have different scale-free topology networks, so it is reasonable to expect that they appear at different thresholds. You could check if it differs much with the s ...
written 12 weeks ago by Lluís R310
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Answer: A: WGCNA - module membership via max kME?
... The genes are assigned to a module using the TOM approach. There is some technical discussion about how does it work in the website of WGCNA. When merging the modules, the gene correlation to the modules also changes! Thus it implies a new module assignment which could be different from what it is ...
written 12 weeks ago by Lluís R310
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Comment: C: GSVA package scores are opposite on mac and windows
... The Bioconductor version (3.6) for R 3.4.2 is not released yet. You seem to be aware that it is on development but the package might change before the release to be consistent between OS. ...
written 3 months ago by Lluís R310
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Comment: C: installing xcms and faahKO package
... The problem seems to come from here: > unable to update packages: boot, Matrix, mgcv You should install it as an admin of your computer to have rights to install/update that packages. Also that might be the reason why you can't install faahKO ...
written 3 months ago by Lluís R310 • updated 3 months ago by Martin Morgan ♦♦ 21k
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Answer: A: WGCNA TOMType specification
... TOMType options handles how should conflicting TOMs be handled (TOM between gene A and B is +, between A and C is +, and between B and C is -), usually there are few conflicts that's why it doesn't make much of a difference. The NetworkType option is described in the adjacency function. There it say ...
written 3 months ago by Lluís R310
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Comment: C: RNseq data for WGCNA
... I think you can add a limit on your module size, or given the TOM distance you could build different networks by cutting at different heights. Maybe there isn't correlation between the group and the traits you are testing. You could also check if building other type of networks adjacency(..., type = ...
written 4 months ago by Lluís R310

Latest awards to Lluís R

Scholar 6 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
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
Voter 7 months ago, voted more than 100 times.
Centurion 9 months ago, created 100 posts.
Scholar 3.0 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 3.0 years ago, voted at least 25 times.

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