User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 172 results • page 1 of 18 • next >
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Answer: A: understanding the meaning boxplot
... From help(boxplot.stats):       The two ‘hinges’ are versions of the first and third quartile,      i.e., close to ‘quantile(x, c(1,3)/4)’.  The hinges equal the      quartiles for odd n (where ‘n <- length(x)’) and differ for even      n.  Whereas the quartiles only equal observations for ‘n % ...
written 8 days ago by Peter Langfelder1.2k
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Comment: C: WGCNA error in network construction ?
... Dear Muhammad, there is no object Expr, you need to use datExpr. It seems that you are new to R and possibly to larger-scale computation and you may benefit from learning more about R and finding someone local who can guide you through some of the pitfalls. You seem to be using an R installation wh ...
written 13 days ago by Peter Langfelder1.2k
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Answer: A: Problem about picking soft threshold power in WGCNA software
... Please read the WGCNA FAQ, particularly point 6. You can use the default power  of 12 since you have hundreds of samples, but do make sure you don't have strong uninteresting sources of variation as described in the FAQ. ...
written 18 days ago by Peter Langfelder1.2k
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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 6 weeks 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 6 weeks 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 6 weeks ago by Peter Langfelder1.2k • updated 6 weeks 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 7 weeks 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 7 weeks 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 8 weeks 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 8 weeks ago by Peter Langfelder1.2k

Latest awards to Peter Langfelder

Scholar 7 weeks ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 13 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 15 months ago, created 100 posts.
Scholar 17 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.5 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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