User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 307 results • page 1 of 31 • next >
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Answer: A: Using WGCNA for purposes other than RNA-SEQ/Microarray
... I'd try to filter on the counts, not on variance, i.e., filter out regions for which the proportion of measurements with number of activated cells bigger than a threshold (say 5) is smaller than a minimum acceptable proportion (e.g., 25%). If you're just log-transforming the data (without other tran ...
written 2 days ago by Peter Langfelder2.1k
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Answer: A: WGCNA sample size minimum: why?
... If you have strong signal and clean data, yes, WGCNA could be informative even with 12 samples. The worst that can happen (with few samples, strong signal and fairly clean data) is that WGCNA won't give you insights that you could not gain from a plain DE analysis. Many of the finer-grain results of ...
written 4 weeks ago by Peter Langfelder2.1k
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Answer: A: WGCNA on methylation data
... I have done a few WGCNA analyses on Illumina 450k methylation data. I used beta values and filtered the data down to about 300k most variant probes. I haven't thought deeply about which transformation is best for methylation data but using beta values worked fairly well. I would not use a log2(beta ...
written 8 weeks ago by Peter Langfelder2.1k
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Comment: C: removing batch effect using DESeq and sva
... I may be missing something, but I don't see why you would want to dichotomize the SVs. You can use limma's removeBatchEffect to remove continuous covariates as well, just put them in the 'covariates' argument. ...
written 8 weeks ago by Peter Langfelder2.1k
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Comment: C: WGCNA with paired samples
... You could do that, just be aware that module eigengenes may not be meaningful since the genes in each module are not necessarily correlated. My experience is that when you have strong driver(s), the eigengene of pretty much any large-enough random group of genes will be strongly associated with the ...
written 10 weeks ago by Peter Langfelder2.1k
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Comment: C: WGCNA with paired samples
... It could happen but it is in my experience not very common, and it is more difficult to detect. ...
written 10 weeks ago by Peter Langfelder2.1k
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Comment: C: Steep dendrograms and few modules. WGCNA on RNA seq data
... I aim for mean connectivity around 100 or less (typically between 30-50); median connectivity usually ends up around 10. ...
written 10 weeks ago by Peter Langfelder2.1k
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Answer: A: Steep dendrograms and few modules. WGCNA on RNA seq data
... The only obvious thing is that the power 5 is quite low for a "signed" network. I would raise it to say 10 or use 'signed hybrid" for network type. However, that may not help you get more modules. You should plot a sample clustering tree and/or PCA plot to make sure you don't have a few large sample ...
written 10 weeks ago by Peter Langfelder2.1k
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Answer: A: Error installing WGCNA for R 3.6 in RStudio Version 1.2.1335
... You seem to be missing the very basic header files that any standard C compiler should have available. I not a Mac user but the previous warning clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot] may have something to do with ...
written 12 weeks ago by Peter Langfelder2.1k
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Comment: C: Adjusting for known covariates before coexpression analysis with WGCNA
... Retained covariates are those whose effect you want to preserve. My understanding is that you want to remove the cell type abundance/composition information, not retain it; removed variables should go into the removedCovariates argument. ...
written 12 weeks ago by Peter Langfelder2.1k

Latest awards to Peter Langfelder

Scholar 4 weeks ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 7 months ago, created an answer that has been accepted. For A: Question about WGCNA soft thresholding value
Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA blockwiseModules parallelisation question
Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: WGCNA: What is `soft thresholding`?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: WGCNA with paired samples
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Appreciated 7 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Appreciated 7 months ago, created a post with more than 5 votes. For A: WGCNA - Signed vs signed hybrid networks
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Theoretical WGCNA Question
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: WGCNA - Signed vs signed hybrid networks
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 9 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Guru 15 months ago, received more than 100 upvotes.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?

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