User: Peter Langfelder

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Posts by Peter Langfelder

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Answer: A: How to know which soft threshold to use for blockwise modules in WGCNA?
... The usual function to determine a suitable soft threshold, pickSoftThreshold, works on (almost) arbitrarily large data sets. It does not need the entire correlation or similarity matrix at once, so it calculates it in smaller pieces which are not the same as the blocks used in blockwiseModules and r ...
written 4 days ago by Peter Langfelder1.4k
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Answer: A: WGCNA - Choosing the best threshold
... You don't say how many genes/transcripts and samples you have in you data set and what conditions this data some from, so it's hard to judge. I personally would be wary of using a power 2 in a regular unsigned network because of the large mean/median connectivities you see in the output. I usually ...
written 23 days ago by Peter Langfelder1.4k
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Comment: C: WGCNA export to cytoscape
... My operational answer is to select a threshold that keeps the file size manageable, then use filtering in Cytoscape to interactively choose a threshold that results in an informative plot. This assumes that Cytoscape is only used for visualization; if you're going to use Cytoscape for further analys ...
written 5 weeks ago by Peter Langfelder1.4k
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Comment: C: WGCNA export to cytoscape
... The weight generated by exportNetworkToCytoscape is exactly the matrix you give it as input. In the tutorials we use TOM but you could also use Pearson correlation or the adjacency. KME is not a measure of edge weight since KME is not a pairwise measure and hence is not used in the exportNetwork... ...
written 5 weeks ago by Peter Langfelder1.4k
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Answer: A: How to select mergeCutHeight in WGCNA?
... I am not aware of a principle from which one could derive an "appropriate" value, but in practice, on data sets with 50-100 samples, using 0.15 to 0.2 has worked fairly well. For fewer samples a larger valuse (0.25 to 0.3) may be warranted. If you want larger modules, increase the value; if you want ...
written 5 weeks ago by Peter Langfelder1.4k
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Answer: A: Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
... There should be no problems with your coding, just be aware that the reported log2foldChange represent fold change with one unit of change in each variable. Since your variables are defined so that different levels correspond to -1 and 1, i.e., the difference is 2, the reported log2 fold changes wil ...
written 11 weeks ago by Peter Langfelder1.4k
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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 3 months ago by Peter Langfelder1.4k
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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 3 months ago by Peter Langfelder1.4k
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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 3 months ago by Peter Langfelder1.4k
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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 3 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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