User: Lluís R

gravatar for Lluís R
Lluís R300
Reputation:
300
Status:
Trusted
Location:
European Union
Last seen:
5 minutes ago
Joined:
2 years, 10 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 161 results • page 1 of 17 • next >
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Comment: C: topGO - Extra terms appearing in main analysis and the enrichment test
... I am not sure, of where do these terms come. You could find the genes present in GOdata for that GO that wheren't originally in your gos.l object, and then find where do they belong. But how are you calculating your weight01_glmpassed to GenTable? As a side note, topGO version in Bioconductor has ma ...
written 9 days ago by Lluís R300
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Answer: A: Pathway analysis from list of differentially expressed genes with fold change, p
... If you have the sample normalized expression you can load it to R and use camera or other tools in limma, or even other gene set enrichment analysis. However as you have the p-values (and I assume the t-values) you can use fgsea to make a GSEA like the one in Broad Institute webpage using the rank o ...
written 14 days ago by Lluís R300
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STATegRa::omicsCompAnalysis invalid 'ncol' value
... I have several problems using the omicsCompAnalysis of STATegRa: When computing the common components with selectCommonComps, the common values are 0. One reason might be that when plotting the ssq the XY or YX component is usually much higher than the variance of X and Y. Looking at the pratios pl ...
stategra written 17 days ago by Lluís R300
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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 20 days ago by Lluís R300
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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 20 days ago by Lluís R300
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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 21 days ago by Lluís R300
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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 21 days ago by Lluís R300
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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 28 days ago by Lluís R300
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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 28 days ago by Lluís R300
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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 7 weeks ago by Lluís R300

Latest awards to Lluís R

Scholar 4 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
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
Voter 5 months ago, voted more than 100 times.
Centurion 7 months ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 2.8 years ago, voted at least 25 times.

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