User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 259 results • page 1 of 26 • next >
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Answer: A: Module preservation WGCNA
... Create a multi-data structure with two copies of your data, perhaps like this: multiExpr = multiData(Set1 = data, Set2 = data) colorList = list(Set1 = colorsmodule) Then run modulePreservation with this input and look at module quality scores in the output (ignore the preservation metrics). Pete ...
written 9 days ago by Peter Langfelder1.6k
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Answer: A: WGCNA following salmon/DESeq2
... I'll second Michael's opinion, and that's also pretty much what I do, except I filter genes using a somewhat different condition. I require that a gene has a relatively high expression (e.g., 0.5 to 1 count per million reads, this translates to a counts in low tens for a typical data set with 30-50M ...
written 17 days ago by Peter Langfelder1.6k
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Comment: C: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
... That's very cool, except the function references mainly Belinda Phipson's PhD dissertation, and the library link provided in the genas help says "This item is currently not available from this repository" (emphasis original). The Majewski et al article does not really explain the method, nor does th ...
written 4 weeks ago by Peter Langfelder1.6k
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Answer: A: Best practices for CRAN package calling a Bioconductor package function
... AFAIK, same as for CRAN packages (my WGCNA package also lives on CRAN but imports functions from a few Bioconductor packages). CRAN includes Bioconductor packages on its package check machines. The only issue is that users cannot simply type install.packages("your package") to install it, they will ...
written 6 weeks ago by Peter Langfelder1.6k
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Comment: C: WGCNA Co-expression network analysis on cuffdiff output
... There's not much advice I can give you - just run a plain WGCNA analysis, and relate the resulting eigengenes to all the pairwise comparisons. If some infections have a very large effect, you may need to run several analyses, one with all infections, then possibly additional analyses with samples wi ...
written 7 weeks ago by Peter Langfelder1.6k
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Comment: C: problem for Using RNA-seq data-set in WGCNA
... Would you please be so kind and read the help page for GOenrichmentAnalysis? The identifiers must be Entrez IDs. Missing Entrez IDs are removed from the enrichment analysis. ...
written 7 weeks ago by Peter Langfelder1.6k
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Comment: C: problem for Using RNA-seq data-set in WGCNA
... LocusLinkID is another name for Entrez ID. You can change all references to LocusLinkID to Entrez, and you will need the Entrez column in your gene annotation table. For this particular piece of code, however, you can use any gene identifier you like (or your enrichment software can use). You could ...
written 8 weeks ago by Peter Langfelder1.6k
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Comment: C: Batch correction when only some subjects have replicates across batches
... Interesting. When you say that batch separation was increased, do you mean separation overall? On the samples from the 3 subjects that were repeated, the batch correction should certainly decrease the batch differences. If not, there's something wrong either with the function or with the way you cal ...
written 9 weeks ago by Peter Langfelder1.6k
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Answer: A: WGCNA: how to change module color
... The colors are just labels. You can use any colors you want. Unfortunately, WGCNA is not set up to let you choose the standard color order. Before telling you how to change the order, I'll just mention that WGCNA does use what you call "standard" colors, the largest modules are labelled turquoise, b ...
written 10 weeks ago by Peter Langfelder1.6k
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Rgraphviz installation fails in R with OpenBLAS
... I am unable to install Rgraphviz_2.24.0 in R 3.5.1 compiled with OpenBLAS. The same package installs fine in R compiled with internal (R) BLAS, so I suspect that the use of external BLAS is to blame here. Any suggestions on how to make the installation succeed? Thanks! The compilation error is Err ...
rgraphviz written 10 weeks ago by Peter Langfelder1.6k

Latest awards to Peter Langfelder

Scholar 6 weeks ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Guru 7 months ago, received more than 100 upvotes.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 18 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Scholar 18 months ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
Scholar 18 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 18 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 18 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 18 months ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 18 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 22 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.6 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.6 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 2.6 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 2.6 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question

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