User: Lluís R

gravatar for Lluís R
Lluís R210
Reputation:
210
Status:
Trusted
Location:
European Union
Last seen:
16 hours ago
Joined:
2 years, 4 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 117 results • page 1 of 12 • next >
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Comment: C: Can I apply WGCNA on unmatched time point microarray data and clinical data?
... You can build the co-expression network and match it with the data you want. What will be harder is the interpretation of the data. Depending what do you want to do you can merge the modules or not. Why would you want to merge modules which are tightly correlated but have different pattern of co-ex ...
written 3 days ago by Lluís R210
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Answer: A: The cor and corp values in verboseScatterplot don't match with cor, corPvalueStu
... verboseScatterplot calculates the p-value of the correlation with corPvalueStudent. corPvalueStudent requires the right number of samples to calculate the correct p-value, is a bit more complex than just the input number of samples.  However the function corAndPvalue calculates the p-value and the c ...
written 3 days ago by Lluís R210
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Comment: C: WGCNA multiple data sets overlapping analysis
... You want to compare how much several networks overlap their modules? You can only compare between two networks to see the overlapping status. So you would need to compare A with B, B with C and A with C, and then extract your conclusions from there. I recommend a venn diagram of the overlapping mod ...
written 7 days ago by Lluís R210
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Comment: C: P values from Deseq Analysis
... When I say "normalize" better I mean if you check for batch effects, or bias by GC content and/or gene length. Also if your design is appropriate and reflects the experiment, (if it is paired, if there are some known co-factors...). At least those are the things I check when using limma. ...
written 13 days ago by Lluís R210
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Answer: A: topGO gene names/ensembl IDs
... topGO accepts the following names: c("entrez", "genbank", "alias", "ensembl", "symbol", "genename", "unigene") So you need to replace the ID = "GeneName" by ID="genename", it has nothing to do with accepting one name of the other but how you pass the argument. ...
written 13 days ago by Lluís R210
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Comment: C: P values from Deseq Analysis
... 1.If you change the threshold for the p-value now you will be doing p-value fishing. There are few genes under your threshold. Period. Probably you might want to analyze the problem, maybe you have very few samples and you need more power, maybe there is batch effect or other confounding factors, or ...
written 14 days ago by Lluís R210
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Comment: C: P values from Deseq Analysis
... 1. If your p-values are between 0 and 1 you also have p-values below 0.05. Or do you mean you have values above 0.05? 2.The p-value indicates the probability to find such values from a given null (H0) hypothesis. You can have a p-value of 0.5 and still the gene is of interest. To report in a paper, ...
written 15 days ago by Lluís R210
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Comment: C: Method to be used in gsva() function
... How does the QuSAGE take into account the covariates? I am used to GSVA and after calculating the scores one can use them with the normal workflow of limma, thus taking into account covariates to estimate the fold-change of pathways. Although the plots of QuSAGE seem appealing ...
written 15 days ago by Lluís R210
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Comment: C: Unable to load package 'hgu95acdf' after upgrading to R 3.4.0
... Oh, I confused the removing with the installing path. Sorry. I agree, I made that for another computer, but in my personal computer I realized too late :( ...
written 21 days ago by Lluís R210
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Comment: C: Unable to load package 'hgu95acdf' after upgrading to R 3.4.0
... I had a similar problem when updating. I am not sure the solution that worked but note that biocLite search for Bioconductor version 3.4 instead of 3.5. I removed biocLite/BiocInstaller from all the paths from the .libPaths() and try using the online one. ...
written 21 days ago by Lluís R210

Latest awards to Lluís R

Centurion 7 weeks ago, created 100 posts.
Scholar 2.3 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 2.3 years ago, voted at least 25 times.

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