User: Lluís R

gravatar for Lluís R
Lluís R180
Reputation:
180
Status:
Trusted
Location:
European Union
Last seen:
19 hours ago
Joined:
2 years, 1 month ago
Email:
l************@gmail.com

Posts by Lluís R

<prev • 82 results • page 1 of 9 • next >
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Answer: A: Comparing across sets of regulated genes -- Strategies?
... You seem to use "regulated" as synonym of with a (significant?) fold change, not of different interactions in the promoter, which could affect to the expression levels, or different interactions at transcription level. One way to see if genes are similarly expressed at both time points would be to ...
written 7 days ago by Lluís R180
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Comment: C: not able to install bioconductor packages
... Then you need to install GenomicRanges too and zlibbioc ...
written 7 days ago by Lluís R180
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Comment: C: not able to install bioconductor packages
... To install packages of Bioconductor use biocLite instead of install.packages to look for the right version in the right repository: source("https://bioconductor.org/biocLite.R") biocLite("airway") Which error message appears when you call library("airway")? ...
written 7 days ago by Lluís R180
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Comment: C: Where can I use the VSN source code in C++?
... The code of the vsn package is partially in R and partially in C++ called into R using Rcpp. If the package wouldn't work as it is it wouldn't be in Bioconductor (for much longer), see the definition of the method in R. I don't understand which R.h files do you expect, or why do you expect having vs ...
written 7 days ago by Lluís R180
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Answer: A: Where can I use the VSN source code in C++?
... The code can be downloaded from the homepage of VSN, or from the github mirror. ...
written 8 days ago by Lluís R180
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Comment: C: Which is the best design matrix to compare a timecourse between two conditions?
... Note that by using coef = ncol(design) in topTable you are extracting the last contrast of the design matrix. Which is not the same between the design1 and the design2. You should probably set different contrast matrix to test the same hypothesis with different designs. ...
written 16 days ago by Lluís R180
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Comment: C: Statistic for GSA
... Yes, but all the function that perform a GSEA from the limma package don't provide the statistic used, as well as other methods don't provide the statistic, hence my question. ...
written 19 days ago by Lluís R180
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Comment: C: Statistic for GSA
... Thanks for your answer, I am aware of the differences and improvements of camera, romer, roast and fry compared to similar methods. But researchers are used to plots from the Broad Institute when they ask for a GSEA, so I would like to show the gene sets found with those functions in a way that they ...
written 19 days ago by Lluís R180
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Statistic for GSA
... There are several packages that implement functions for a Gene Set (Enrichment) Analysis, some of them are limma, gsar, gsva, piano, fgsea, pgsea. However I couldn't find an agreement for those tests which accept any statistic as input: fgsea, runGSA, geneSetTest. Using plotting functions, like plo ...
gsa gsea concept written 20 days ago by Lluís R180 • updated 19 days ago by Pekka Kohonen180
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... How do you loaded DF_sim to R? Have you checked if isSymmetric(DF_sim) returns the same error? Could you provide the traceback of the error? It could be that the error tolerance is lower than the difference in the matrix, you could then change the error tolerance or make it symmetric as Peter says. ...
written 20 days ago by Lluís R180

Latest awards to Lluís R

Scholar 2.1 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 2.1 years ago, voted at least 25 times.

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