User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 221 results • page 1 of 23 • next >
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Answer: A: WGCNA: intrepreting grey unassigned "module"?
... I am surprised that you only see 55 genes DE between the two species, but maybe that's the biology. I would double-check that there were no batch effects or other technical effects. You could make the module identification more relaxed, e.g. lower the minimum module size and/or increase deepSplit; i ...
written 7 hours ago by Peter Langfelder1.4k
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Answer: A: WGCNA: intrepreting grey unassigned "module"?
... I have not seen your data and analysis so it's difficult to make definitive statements, but I would be suspicious if the genes different between species were (mostly) in the grey module. I would expect the that inter-species differences are the biggest source of variation in the data and hundreds if ...
written 11 hours ago by Peter Langfelder1.4k
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Answer: A: novice: building gene co-expression network using RNA-Seq data
... I would not use the "distance" adjacency type, which uses Euclidean distance instead of correlation. Distance is more appropriate for calculating (dis-) similarities of samples, not of genes. Just leave the adjacency type either default (unsigned network), or use type = "signed hybrid".  If you want ...
written 1 day ago by Peter Langfelder1.4k
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Answer: A: Error with the tutorial for the WGCNA package
... Thanks for the bug report, I will fix this in the next WGCNA update. In the meantime, I suggest you take a look at the anRichment package (https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/GeneAnnotation/) which provides a replacement for GOenrichmentAnalysis. Please look through the ...
written 7 days ago by Peter Langfelder1.4k
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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 15 days ago by Peter Langfelder1.4k
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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 18 days ago by Peter Langfelder1.4k
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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 4 weeks ago by Peter Langfelder1.4k
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Comment: C: Limma-voom with external observation weights
... Thanks for the clarification. ...
written 4 weeks ago by Peter Langfelder1.4k
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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 4 weeks ago by Peter Langfelder1.4k
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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 4 weeks ago by Peter Langfelder1.4k • updated 4 weeks ago by Gordon Smyth33k

Latest awards to Peter Langfelder

Scholar 14 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 24 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 24 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 24 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 24 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.2 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 2.4 years ago, created 100 posts.
Scholar 2.5 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 3.6 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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