User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 252 results • page 1 of 26 • next >
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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 4 days 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 days 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 11 days ago by Peter Langfelder1.6k
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Answer: A: TOMplot error: "color" is not a graphical parameter (WGCNA)
... The relevant argument in TOMplot is Colors, not colors. Try supplying Colors, not colors. Peter ...
written 13 days ago by Peter Langfelder1.6k
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Answer: A: Batch correction when only some subjects have replicates across batches
... I'm not sure my answer will be helpful since I don't quite follow the variance and weight issues raised by Aaron and may be missing some important aspects here. Take it for what it's worth... You can try a developmental version of WGCNA from here (dropbox link). To install it, you will need to be a ...
written 18 days ago by Peter Langfelder1.6k
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Comment: C: WGCNA Co-expression network analysis on cuffdiff output
... It's not clear what your goal (research question you are trying to answer) is. For most data sets that I normally come across you would not run 28 different WGCNA analyses (unless you have 1000+ samples); you would run one or perhaps a few different WGCNA analyses and then relate modules to pairwise ...
written 29 days ago by Peter Langfelder1.6k
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Comment: C: Segfault error when loading WGCNA
... I suggest posting this issue on the R-users list (https://www.r-project.org/mail.html). As Luis suggested, try installing the latest version of R since the maintainers of R may not be willing to look into an older version. I personally don't see this bug, but I also don't use CentOS. Personally, I ...
written 5 weeks ago by Peter Langfelder1.6k
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Answer: A: How to interpret WGCNA exported result?
... You would want to export the WGCNA results as described in WGCNA tutorial I, section 3d. You can sort the genes by kME in the interesting module, which gives you the top hub genes. The export to Cytoscape is more for visualization or if you want to further analyze the network in Cytoscape. ...
written 6 weeks ago by Peter Langfelder1.6k
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Answer: A: DESeq2 - is VSD data normalized for covariates in the model
... No, VST data is not corrected for covariates. Your question seems to mix VST and normalized counts, which are not the same. VST data are similar to normalized and log-transformed counts, so they can be thought of being on a log scale. You can correct VST data for covariates by running a simple lin ...
written 7 weeks ago by Peter Langfelder1.6k
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Answer: A: WGCNA extract genes from a module
... Regarding the WGCNA website, sorry for the missing files, here's the new address: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ You can follow the tutorial there. Extracting the genes in a module is described in Tutorial I, section 3d. Peter     ...
written 7 weeks ago by Peter Langfelder1.6k

Latest awards to Peter Langfelder

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Guru 5 months ago, received more than 100 upvotes.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 16 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Scholar 16 months ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
Scholar 16 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 16 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 16 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 16 months ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 16 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 20 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.5 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.5 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 2.5 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Teacher 2.5 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 - Signed vs signed hybrid networks
Scholar 2.7 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 2.9 years ago, created 100 posts.

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