User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 210 results • page 2 of 21 • next >
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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 4 months ago by Peter Langfelder1.4k
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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 4 months ago by Peter Langfelder1.4k
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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 4 months ago by Peter Langfelder1.4k
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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 4 months ago by Peter Langfelder1.4k
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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 4 months ago by Peter Langfelder1.4k
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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 4 months ago by Peter Langfelder1.4k
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Comment: C: RNseq data for WGCNA
... The link to data is invalid (box reports the file has been removed or is unavailable). Plot a sample tree from the "Expr" data; you may have a monstrous batch effect. I hope the raw counts are really raw counts, not some transformed version. Your filter seems too stringent to me, I would filter on ...
written 4 months ago by Peter Langfelder1.4k
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Answer: A: RNseq data for WGCNA
... It is impossible to diagnose issues with your data or analysis without seeing the data (the code looks reasonable but it obviously isn't complete). One usually sees at least a few distinct branches in WGCNA analysis of expression data, but again, without knowing what your data represent and seeing t ...
written 5 months ago by Peter Langfelder1.4k
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Answer: A: WGCNA connecting trait data
... Add a "drop = FALSE" to this line: datTraits = allTraits[traitRows, -1] datTraits = allTraits[traitRows, -1, drop = FALSE] Your allTraits contains only 2 columns; when you remove the first one, you are left with just one column and R converts that into a single vector unless you add the drop = FAL ...
written 5 months ago by Peter Langfelder1.4k
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Answer: A: WGCNA works on time course data
... It depends on what your research aims/questions are. However, since you only seem to have a total of 7*4=28 samples, I would construct one network from all samples. If you find that the largest driver of variability is uninteresting, adjust the data for it and construct a new network. ...
written 6 months ago by Peter Langfelder1.4k

Latest awards to Peter Langfelder

Scholar 12 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 22 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 22 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 22 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 22 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.0 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 2.2 years ago, created 100 posts.
Scholar 2.3 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 3.4 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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