User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 227 results • page 2 of 23 • next >
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Answer: A: Inconsistent RNAseq data in knockdown expt
... When you check DE of a single mRNA or two, you don't need to look at padj; the unadjusted p-value (and perhaps fold change) is appropriate in this case. (FDR is appropriate when you you test whether any of a large number of tests are significant.) ...
written 11 weeks ago by Peter Langfelder1.5k
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Answer: A: What does this error mean? - issue implementing SVA
... If I remember correctly, it means that one of your variables (genes/transcripts) is perfectly correlated with trait, or is constant, and its corresponding association p-value with the trait is either infinite or NaN/NA. Filter out any constant genes (usually genes with all zeros); you may have to fi ...
written 11 weeks ago by Peter Langfelder1.5k
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Answer: A: DESeq LRT test and construction of Co-expression network
... If you intend to WGCNA to construct the co-expression network, please read the WGCNA FAQ (https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html). The biggest issue is your low sample number, 6 samples is too few to run WGCNA on. We don't recommend filtering genes by dif ...
written 3 months ago by Peter Langfelder1.5k
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Comment: C: Limma-voom with external observation weights
... Thanks for the clarification. ...
written 3 months ago by Peter Langfelder1.5k
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Comment: C: Limma-voom with external observation weights
... Thanks! If I may ask a second question, for designs without replicates (e.g., when there's a continuous covariate), is limma-voom a more appropriate option than edgeR or similar approaches that need dispersion estimation for each condition? Voom seems to use a single mean-variance function (for all ...
written 3 months ago by Peter Langfelder1.5k
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Limma-voom with external observation weights
... I'd like to use limma-voom to do a differential expression analysis on RNA-seq data using "my own" (i.e., external for limma) observation weights that downweigh outliers and which are different from voom weights. (I have a way to calculate the weights, that's not the issue). The user's guide and hel ...
limma limma-voom written 3 months ago by Peter Langfelder1.5k • updated 3 months ago by Gordon Smyth33k
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Answer: A: Differential Coexpression Analysis
... Searching for "differential coexpression" brings out several articles describing different ways of doing a differential co-expression analysis. WGCNA is not designed for gene-level differential co-expression analysis, but you can certainly study preservation of modules as well as common (consensus) ...
written 3 months ago by Peter Langfelder1.5k
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Answer: A: How to know which soft threshold to use for blockwise modules in WGCNA?
... The usual function to determine a suitable soft threshold, pickSoftThreshold, works on (almost) arbitrarily large data sets. It does not need the entire correlation or similarity matrix at once, so it calculates it in smaller pieces which are not the same as the blocks used in blockwiseModules and r ...
written 4 months ago by Peter Langfelder1.5k
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Answer: A: WGCNA - Choosing the best threshold
... You don't say how many genes/transcripts and samples you have in you data set and what conditions this data some from, so it's hard to judge. I personally would be wary of using a power 2 in a regular unsigned network because of the large mean/median connectivities you see in the output. I usually ...
written 4 months ago by Peter Langfelder1.5k
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Comment: C: WGCNA export to cytoscape
... My operational answer is to select a threshold that keeps the file size manageable, then use filtering in Cytoscape to interactively choose a threshold that results in an informative plot. This assumes that Cytoscape is only used for visualization; if you're going to use Cytoscape for further analys ...
written 5 months ago by Peter Langfelder1.5k

Latest awards to Peter Langfelder

Teacher 12 months ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 12 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Scholar 12 months ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
Scholar 12 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 12 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 12 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 12 months ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 12 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 16 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.3 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 2.5 years ago, created 100 posts.
Scholar 2.6 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 3.8 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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