User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 227 results • page 1 of 23 • next >
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Answer: A: WGCNA grey module
... There is no limit on the size of any module or the number of the grey genes from the point of view of WGCNA itself. How many genes should end up grey depends a lot on how many genes are in the analysis to begin with and how they were filtered, how selective the analyst wants to be in the module defi ...
written 4 weeks ago by Peter Langfelder1.5k
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Comment: C: WGCNA Analysis and Hub gene analysis
... You need to be more specific in your questions. How do you define "relevant" modules? Enrichment analysis in functional sets (GO, KEGG) etc could help you identify modules that may have some functional interpretation. I am not sure what you mean by gene "expressed in all 4 tissues" - if it's really ...
written 5 weeks ago by Peter Langfelder1.5k
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Comment: C: rlog not found
... Well, that was a quick fix! So the OP should be able to install GenomeInfoDb and try again, and if that doesn't work, I would reinstall everything. ...
written 6 weeks ago by Peter Langfelder1.5k
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Comment: C: rlog not found
... Hmm.. there seems to be one on the package page https://www.bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html - or am I missing something? ...
written 6 weeks ago by Peter Langfelder1.5k
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Comment: C: rlog not found
... First question is, did you (or whoever installed R) copy the packages over? R does not copy packages from older installations by itself. The safest way to fix a broken installation is to uninstall R, remove your personal library (which is usually the culprit) - your personal R library usually sits ...
written 6 weeks ago by Peter Langfelder1.5k
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Comment: C: rlog not found
... Perhaps you installed R-3.5.0 and copied over packages installed from a previous version?   ...
written 6 weeks ago by Peter Langfelder1.5k
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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 8 weeks ago by Peter Langfelder1.5k
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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 8 weeks ago by Peter Langfelder1.5k
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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 8 weeks ago by Peter Langfelder1.5k
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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 9 weeks 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 2.3 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 3.7 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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