User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 161 results • page 1 of 17 • next >
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Answer: A: Question about WGCNA soft thresholding value
... The negative "signed R^2" is negative when your network has more genes with high connectivity than ones with low connectivity (i.e., the regression line for the fit log(n(k))~log(k) has a positive slope). It means your network shows a topology in some ways opposite (more high connectivity than low c ...
written 3 days ago by Peter Langfelder1.1k
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Answer: A: WGCNA error : Error in hclust
... I don't see why log2(x+1) should cause any trouble. It certainly does not cause any trouble with the data I use. Inspect the transformed data - are all entries of the 4 genes you sent finite after the transformation? ...
written 7 days ago by Peter Langfelder1.1k
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Answer: A: WGCNA error : Error in hclust
... I assume you have transposed the expression data before you calculate adjacency (WGCNA requires samples in rows and genes in columns). I took your data, loaded it into R and am getting no missing or NaN results, so your description or code are missing something. Here's the data I have, transposed i ...
written 8 days ago by Peter Langfelder1.1k
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Answer: A: WGCNA analysis with NCBI GEO Series Matrix file?
... I would try to use the GEOQuery to download the data and split them into expression and sample data tables. You then need to make sure the expression data were normalized in a usable way. Then, as Luis said, follow the WGCNA tutorials. ...
written 10 days ago by Peter Langfelder1.1k
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Answer: A: WGCNA error : Error in hclust
... Well, I would run adj = adjacency(datExpr) and check whether there are any missing or NaN values. If there are any, get theirs rows and/or columns, and check the corresponding columns in datExpr (check their variance). Also make sure you run the most recent version of WGCNA. I don't have any oth ...
written 10 days ago by Peter Langfelder1.1k
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Answer: A: WGCNA error : Error in hclust
... My guess is that your data contain some non-varying (constant) genes. Try running goodSamplesGenes on datExpr, then check the component allOK of the result. If that is FALSE, you will need to remove genes with zero variance as illustrated in section 1b of Tutorial I of the WGCNA tutorials. ...
written 11 days ago by Peter Langfelder1.1k
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Answer: A: WGCNA Co-expression
... Some people do it despite (or not knowing) our recommendation, perhaps they have good reasons to do so. Still, the general recommendation is not to filter genes by DE. I suggest you work through the tutorials and run your own analysis along the lines of the tutorial. ...
written 20 days ago by Peter Langfelder1.1k
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Answer: A: WGCNA Co-expression
... Please read WGCNA FAQ, item 2, at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html We don't recommend filtering genes by differential expression. As for using WGCNA, there are several tutorials at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpacka ...
written 21 days ago by Peter Langfelder1.1k
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Answer: A: Wired modules WGCNA cluster dendrogam
... The power of 20 is fairly high but not unreasonably so if you are constructing a signed network and you have less than 20 samples). Otherwise I suggest you follow the advice in WGCNA FAQ, item 6. https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html As I said, there's ...
written 5 weeks ago by Peter Langfelder1.1k
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Answer: A: Wired modules WGCNA cluster dendrogam
... It means you have a pair of genes with high similarity (dissimilarity 0.4, so similarity 0.6) while all other genes have higher dissimilarities. Apriori nothing wrong with that although in most gene expression studies I do see somewhat smaller dissimilarities (many genes pairs reaching down to 0.75 ...
written 6 weeks ago by Peter Langfelder1.1k

Latest awards to Peter Langfelder

Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 13 months ago, created 100 posts.
Scholar 14 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?

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