User: Peter Langfelder

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Posts by Peter Langfelder

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Answer: A: SampleNetwork in WGCNA
... Apologies for that, UCLA just changed the server and folders for our web pages... here's the new address: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/SampleNetwork/ Hope you find it useful! Peter ...
written 4 days ago by Peter Langfelder1.5k
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Comment: C: accounting for technical variation in DESEQ2
... No, I recommend checking the normalized (and perhaps VST'd) data and unless there is good reason to worry about quantile normalization, don't (worry about QN). As Michael says below, if you feel you have inter-sample technical variation, you can look into SVA, RUV-seq and possibly other approaches t ...
written 7 days ago by Peter Langfelder1.5k
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Answer: A: accounting for technical variation in DESEQ2
... Others may have more systematic answers, but here are my 2 cents regarding specifically quantile normalization. When I check quantiles in DESeq-normalized data (more precisely, normalized and variance-stabilized), the data always look "nearly quantile normalized", in that specific percentiles (I nor ...
written 7 days ago by Peter Langfelder1.5k
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Comment: C: WGCNA: Understanding module-trait correlations
... The default in WGCNA is, for historical reasons, unsigned network (at least for most functions). You need to check the help file for each function you want to use; most functions where network type matters will have an argument networkType or just type. TOM type is not related to network type and o ...
written 7 days ago by Peter Langfelder1.5k
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Comment: C: WGCNA: Understanding module-trait correlations
... You got it exactly right. I would only add that instead of running an unsigned analysis, I personally prefer to run a signed or signed hybrid, and then look at whether anti-correlated modules could be thought of as part of a single biological pathway/process. In my work, negatively correlated module ...
written 8 days ago by Peter Langfelder1.5k
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Comment: C: WGCNA: Understanding module-trait correlations
... Apologies for the late reply. We recommend using a signed or signed hybrid network analysis. You can read some more here: http://www.peterlangfelder.com/signed-or-unsigned-which-network-type-is-preferable/ and http://www.peterlangfelder.com/two-types-of-signed-networks-in-wgcna/ Peter ...
written 14 days ago by Peter Langfelder1.5k
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Comment: C: WGCNA: Understanding module-trait correlations
... There are two different correlations (or sets of correlations) that you need to distinguish. The eigengene-trait correlation measures the strength and direction of association between the module (more precisely, the representative profile) and the trait. If this is positive (negative), it means the ...
written 14 days ago by Peter Langfelder1.5k
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Answer: A: WGCNA: Understanding module-trait correlations
... Your question is not very clear but I'll try anyway. The module-trait heatmap usually represents the correlations of the module eigengenes with traits. When that correlation is high, it means the eigengene increases with increasing trait. In a signed network (where all genes in a module are positive ...
written 17 days ago by Peter Langfelder1.5k
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Comment: C: How to create "trait data" file for WGCNA
... It depends on what question you want to ask. Do you want to see modules that relate to each treatment group vs. controls? Then create one variable for each treatment group. Call the variables groupVar1, groupVar2, groupVar4, groupVar8. Define the groupVar1 [2,4,8] variable to be 1 if the sample is t ...
written 4 weeks ago by Peter Langfelder1.5k
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Comment: C: problem for Using RNA-seq data-set in WGCNA
... Change the line probes2annot = match(probes,GeneAnnotation$substanceBXH) to probes2annot = match(probes,GeneAnnotation$gene_id)   You may also want to change ProbeID=names(datExprFemale), GeneAnnotation[probes2annot,] to just GeneAnnotation[probes2annot, c("gene_id", "gene_name")] and you ...
written 6 weeks ago by Peter Langfelder1.5k

Latest awards to Peter Langfelder

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Guru 12 weeks ago, received more than 100 upvotes.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 14 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Scholar 14 months ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
Scholar 14 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 14 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 14 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 14 months ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 14 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 18 months 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?
Scholar 2.3 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.3 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 2.3 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.5 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 2.7 years ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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