User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 169 results • page 1 of 17 • next >
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Answer: A: How to adjust the parameters of WGCNA
... I'm not sure I understand your question well, but if you get two opposite expression patterns in one module, chances are it's because you have constructed an unsigned network. Rerun WGCNA using a signed or 'signed hybrid' network. I recommend 'signed hybrid' with the same soft thresholding power as ...
written 15 days ago by Peter Langfelder1.2k
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Comment: C: Bug in vsn2 in package vsn?
... Thanks - I will report whatever nuggets of wisdom I can find... ...
written 15 days ago by Peter Langfelder1.2k
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Bug in vsn2 in package vsn?
... Unless I'm missing something, there seems to be a bug in the variance stabilization function vsn2 or the predict method for the vsn object when calib="none". Below is a self-contained example with random data. Thanks! >#Simulate data >library(vsn); > nGenes = 1000; > nSamples = 100; &g ...
vsn vsn2 written 17 days ago by Peter Langfelder1.2k • updated 15 days ago by Wolfgang Huber12k
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Answer: A: ExportingWGCNA data for Ingenutity IPA
... I haven't worked much with IPA but it is my understanding that IPA requires a simple list of genes, and will create the network(s) from connections curated from the literature. In contrast, Cytoscape and VisANT need the network information as input, hence the need for specific network export functio ...
written 22 days ago by Peter Langfelder1.2k
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Answer: A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... It means your matrix is not exactly symmetric. Symmetrize it using (DF_mat + t(DF_mat))/2 then try again. ...
written 24 days ago by Peter Langfelder1.2k
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Answer: A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... Please run max(abs(DF_mat - t(DF_mat)), na.rm = TRUE) Check the result; the code throws the error because this number is greater than 1e-12. ...
written 25 days ago by Peter Langfelder1.2k
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Answer: A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... Try DF_mat = as.matrix(DF_sim), then run the function again on DF_mat. HTH, Peter ...
written 25 days ago by Peter Langfelder1.2k
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Answer: A: WGCNA small number of genes
... Indeed, with a small number of genes you are not likely to construct a scale-free network, but the heterogeneity probably plays a large part as well. I suggest you read through the WGCNA FAQ, especially points 2, 5, and 6 (but other parts of the FAQ can be helpful as well). Use a soft thresholding p ...
written 26 days ago by Peter Langfelder1.2k
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Answer: A: Question about WGCNA soft thresholding value
... The negative "signed R^2" is negative when your network has more genes with high connectivity than ones with low connectivity (i.e., the regression line for the fit log(n(k))~log(k) has a positive slope). It means your network shows a topology in some ways opposite (more high connectivity than low c ...
written 5 weeks ago by Peter Langfelder1.2k
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Answer: A: WGCNA error : Error in hclust
... I don't see why log2(x+1) should cause any trouble. It certainly does not cause any trouble with the data I use. Inspect the transformed data - are all entries of the 4 genes you sent finite after the transformation? ...
written 6 weeks ago by Peter Langfelder1.2k

Latest awards to Peter Langfelder

Scholar 24 days ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 10 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 10 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 10 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 10 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 12 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 14 months ago, created 100 posts.
Scholar 16 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.4 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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