User: Peter Langfelder

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Posts by Peter Langfelder

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Answer: A: Error in intramodularConnectivity(ADJ1, colorh1) : object 'colorh1' not found
... Your code probably does not define colorh1 anywhere before you attempt to use it in your code that you posted. But there's no way to tell because you did not post a reproducible example or at least full code. (If the above is the full code, it clearly misses the definition of colorh1.) It is best t ...
written 17 days ago by Peter Langfelder1.8k
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Answer: A: DESeq2: error, the model matrix is not full rank, linear combinations
... You get this error because the sum of all s variables gives the intercept column: xx = apply(colData, 2, as.numeric) rowSums(xx[, 1:6]) Intercept is part of the model matrix unless you include -1 in the model specification. In this case, you need to either specify -1 or remove one of the s ...
written 27 days ago by Peter Langfelder1.8k
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Answer: A: WGCNA Parameter Enforcement Stymied by Prior Batch-normalization of Multi-cohort
... As far as the discrepancy between kME and assigned module is concerned, there are two potential sources of this. One is the use of topological overlap instead of adjacency as the similarity on which clustering is based. You can switch to adjacency using TOMType = "none" for blockwiseModules. The sec ...
written 27 days ago by Peter Langfelder1.8k
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Answer: A: Consensus modules preservation WGCNA
... Yes, you have two reference data sets and one test data set. Run module preservation between each of the reference data sets and the test data set, so you get two sets of preservation statistics. You can look for modules for which the preservation is low in both preservation calculations. My intuit ...
written 4 weeks ago by Peter Langfelder1.8k
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Answer: A: Module membership vs gene significance does not correlate (WGCNA)
... First, make sure that it's not a trivial mistake of plotting a different module or trait than the combination that has a high correlation. If that has been checked, lack of GS-MM correlation could indicate that only a submodule relates to the trait. In that case, perhaps redoing the analysis with a ...
written 5 weeks ago by Peter Langfelder1.8k
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Answer: A: Correlate WGCNA modules from 2 separate analyses (small and large RNA)
... Yes, you can correlate module eigengenes from different analyses (across common samples), just as you could correlate the expression levels of single short and long mRNAs. I would not compare subleading principal components without a good rationale to believe that they represent something meaningful ...
written 7 weeks ago by Peter Langfelder1.8k
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Comment: C: WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are n
... Glad you got it worked out. ...
written 7 weeks ago by Peter Langfelder1.8k
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Comment: C: WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are n
... Strange. The function consensusTOM works in my installation. I would double-check that the new package was compiled and installed from source and that there is no confusion between a system-wide and personal library. It does look like your installation mixes new R code with old compiled code. ...
written 8 weeks ago by Peter Langfelder1.8k
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Answer: A: WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are n
... Indeed, this is a bug in the current WGCNA version, thanks for reporting it. I fixed it in a development version and posted the tarball on dropbox at this link: [https://www.dropbox.com/s/lganlp7h41tg06n/WGCNA_1.66-90.tar.gz?dl=0][1]. If you are able to install source packages, please give it a try ...
written 8 weeks ago by Peter Langfelder1.8k
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Answer: A: Enrichment Analysis with only GeneSymbols
... If standard gene sets like GO or KEGG is all you want, you could simply upload your genes to DAVID ([https://david.ncifcrf.gov/][1]). I believe DAVID will accept just gene symbols. I don't have a Bioconductor-only solution, but if you're willing to give it a try, anRichment ([https://horvath.genetic ...
written 8 weeks ago by Peter Langfelder1.8k

Latest awards to Peter Langfelder

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 5 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
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 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 11 months ago, received more than 100 upvotes.
Scholar 22 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Teacher 22 months ago, created an answer with at least 3 up-votes. 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
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 22 months ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
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 - soft threshold
Scholar 22 months ago, created an answer that has been accepted. For A: How to know which soft threshold to use for blockwise modules in WGCNA?
Scholar 22 months ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 22 months ago, created an answer that has been accepted. For A: How to get an output from DESeq2 to be used in WGCNA package
Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 3.0 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 3.0 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 3.0 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 3.0 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 3.2 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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