User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 312 results • page 1 of 32 • next >
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Comment: C: DeSeq2 Design (A-B)-(C-D)
... If I understand your aim correctly, you want something like pheno.ext = data.frame( AB.vs.CD = as.numeric(Experiment_Groups %in% c(A, B)), AC.vs.BD = as.numeric(Experiment_Groups %in% c(A, C))) Then run DESeq2 or limma on your data, the pheno.ext data frame as colDat ...
written 9 days ago by Peter Langfelder2.2k
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Answer: A: Subset WGCNA results for export to Cytoscape
... The simplest solution is to calculate TOM only for the module genes, as Andres suggested. A slight drawback is that the TOM within the module may be slightly different from TOM calculated from all data (or at least data from the relevant block). An alternative is to use the function vectorTOM which ...
written 10 days ago by Peter Langfelder2.2k
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Answer: A: WGCNA: 1) low soft thresholding power, 2) large modules, 3) best correlation for
... I'd go with 6 for unsigned or signed hybrid networks, and 12 for signed network. Power 3 is really too low with 55 samples. As Andres mentioned, check the sample clustering tree for large drivers (strong branches); large modules are often the result of having very strong global drivers of expression ...
written 23 days ago by Peter Langfelder2.2k
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Answer: A: WGCNA soft threshold with methylation data but no scale-free topology
... (duplicate post deleted, sorry) ...
written 6 weeks ago by Peter Langfelder2.2k
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Answer: A: WGCNA soft threshold with methylation data but no scale-free topology
... Mean connectivity in the several thousands is a bit too high; I would investigate whether the samples cluster in strong clusters and if so, would probably adjust for the cluster membership. You may also want to adjust for age and sex of the donors, if you have that information. If you don't see anyt ...
written 6 weeks ago by Peter Langfelder2.2k
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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 8 weeks ago by Peter Langfelder2.2k
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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 12 weeks ago by Peter Langfelder2.2k
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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 3 months ago by Peter Langfelder2.2k
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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 3 months ago by Peter Langfelder2.2k
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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 4 months ago by Peter Langfelder2.2k

Latest awards to Peter Langfelder

Scholar 12 weeks ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 9 months ago, created an answer that has been accepted. For A: Question about WGCNA soft thresholding value
Scholar 9 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 9 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 9 months ago, created an answer that has been accepted. For A: WGCNA blockwiseModules parallelisation question
Scholar 9 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 9 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: WGCNA: What is `soft thresholding`?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
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 9 months ago, created an answer with at least 3 up-votes. For A: WGCNA with paired samples
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Appreciated 9 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Appreciated 9 months ago, created a post with more than 5 votes. For A: WGCNA - Signed vs signed hybrid networks
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Theoretical WGCNA Question
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: WGCNA - Signed vs signed hybrid networks
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
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 17 months ago, received more than 100 upvotes.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?

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