User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 305 results • page 1 of 31 • next >
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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 6 days 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 days 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 19 days 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 21 days 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 21 days 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 22 days 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 4 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 4 weeks ago by Peter Langfelder2.1k
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Answer: A: Adjusting for known covariates before coexpression analysis with WGCNA
... It is my understanding that ComBat cannot handle continuous nuisance variables (i.e., variables you want to remove). It can handle continuous covariates which in this case means variables whose effect you want to keep; these are supplied in the 'mod' argument for ComBat. For removing the effect of ...
written 4 weeks ago by Peter Langfelder2.1k
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Answer: A: Error in sizeRestrictedClusterMerge: replace is not a multiple of replacement le
... I forgot to mention that you may be able to avoid this error by changing the argument maxBlockSize (which I do recommend adjusting to the largest value your machine can take). I will of course try to track it down and fix it though. ...
written 4 weeks ago by Peter Langfelder2.1k

Latest awards to Peter Langfelder

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Guru 13 months ago, received more than 100 upvotes.
Scholar 2.0 years ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 2.0 years ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
Scholar 2.0 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.0 years ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 2.0 years ago, created an answer that has been accepted. For A: How to know which soft threshold to use for blockwise modules in WGCNA?
Scholar 2.0 years ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 2.0 years ago, created an answer that has been accepted. For A: How to get an output from DESeq2 to be used in WGCNA package
Scholar 2.4 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 3.2 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 3.2 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 3.2 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 3.2 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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