User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 204 results • page 1 of 21 • next >
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Comment: C: WGCNA with distance matrix only from newick data.
... The simplest way of turning a distance matrix into a similarity consists of two steps. First, scale the distances to lie between 0 and 1, e.g. by dividing the distances by their maximum or by taking tanh() of the distance matrix (perhaps scaled by some characteristic distance, e.g. mean or 2*mean). ...
written 7 days ago by Peter Langfelder1.3k
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Answer: A: WGCNA with distance matrix only from newick data.
... If you only have the distance matrix, you cannot get the expression profile of anything, be it the eigengene or the intramodular hub genes. But you can identify which genes are the intramodular hub genes. Run the function intramodularConnectivity and for each module identify the gene or a few genes ...
written 12 days ago by Peter Langfelder1.3k
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Answer: A: WGCNA - module membership via max kME?
... It is hard to say why you don't get more genes in modules (it's like asking "why does my experiment not work" without actually telling people what you did in your experiment), but perhaps you should look into how many genes are actually detected (have counts > 0) in each cell, and how many genes ...
written 20 days ago by Peter Langfelder1.3k
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Answer: A: WGCNA - module membership via max kME?
... First things first: grey is not really a module, it is a label for unassigned genes, and the eigengene and kME for the grey "module" are more or less meaningless. In other words, ignore the eigengene and kME values for the grey "module". WGCNA assigns module labels using dynamic tree cut (look up d ...
written 26 days ago by Peter Langfelder1.3k
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Answer: A: Error in plot.new() : figure margins too large
... To the OP's question, the error usually means the plotting window, or the current plot area of  a plot window, is too small to accommodate the requested plot margins. The fix may be as easy as enlarging the plot window but you may have to modify the  the margins and lhei, lwid arguments. See ?heatma ...
written 5 weeks ago by Peter Langfelder1.3k
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Answer: A: GSVA package scores are opposite on mac and windows
... I would guess that SVA uses singular value decomposition (SVD); in SVD, the sign of the singular vectors is arbitrary and may change between implementations. Here's a quote from help(svd):      Recall that the singular vectors are only defined up to sign (a      constant of modulus one in the compl ...
written 6 weeks ago by Peter Langfelder1.3k
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Comment: C: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
... It is a relatively new function, and it was not widely (in fact, at all) advertised. ...
written 7 weeks ago by Peter Langfelder1.3k
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Answer: A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
... To my knowledge, there's no way to use ComBat to adjust for continuous variables. The WGCNA package (over on CRAN) has an implementation of Empirical Bayes-moderated linear model regression (function empiricalBayesLM) that works with either continuous or categorical variables but unlike ComBat, it d ...
written 7 weeks ago by Peter Langfelder1.3k
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Answer: A: How to get an output from DESeq2 to be used in WGCNA package
... Please read WGCNA FAQ at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html , especially points 3 and 4, but the rest my also be useful. Also, if you are new to WGCNA, please follow WGCNA tutorials at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackag ...
written 7 weeks ago by Peter Langfelder1.3k
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Answer: A: WGNA export to external software
... It is most likely a bug in WGCNA compiled code. How big is your data? If you can, please download and install on your cluster this WGCNA development version in which the bug may be fixed: https://www.dropbox.com/s/hl49yc0l58nkp36/WGCNA_1.61-84.tar.gz?dl=0 Download the file and in R type install.p ...
written 7 weeks ago by Peter Langfelder1.3k

Latest awards to Peter Langfelder

Scholar 9 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 19 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 19 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 19 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 19 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 21 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 21 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 23 months ago, created 100 posts.
Scholar 2.1 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 3.2 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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