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User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 273 results • page 1 of 28 • next >
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Answer: A: WGCNA - confounding effect based on technical variables (some continuous)
... It's a bit difficult to give meaningful answers without seeing the data and the specific questions, but here are a few options. If the modules are expected to be present (i.e., the constituent genes are expected to be correlated) within each run, you can do a consensus WGCNA between the two batche ...
written 6 days ago by Peter Langfelder1.7k
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Answer: A: WGCNA soft threshold power showing very strange values
... I recommend reading the relevant part of [WGCNA FAQ][1], especially question 6. I don't have any experience with metagenomic data, so I can't give you a more informed answer, but it is always helpful to plot the sample clustering tree and/or PCA plot to make sure nothing weird is going on. [1]: ...
written 12 days ago by Peter Langfelder1.7k
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Comment: C: Deviance returned by DESeq2
... OK, the issue is that -2 times the log likelihood needs the -2LL(saturated model) subtracted out before it can be used as a quality of fit statistic (if at all). Which not hard to do with the existing output. If I might make a request/suggestion, it would be great to add an additional column to the ...
written 20 days ago by Peter Langfelder1.7k
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Comment: C: Deviance returned by DESeq2
... Thanks. (I think you meant -2 * dnbinom(2^(1:10), mu=2^(1:10), size=1/.05, log=TRUE). ...
written 20 days ago by Peter Langfelder1.7k
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Comment: C: Deviance returned by DESeq2
... Apologies, I neglected to copy the relevant part from DESeq2 guide: library("DESeq2") dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition) Peter ...
written 20 days ago by Peter Langfelder1.7k
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Deviance returned by DESeq2
... This may be more of a statistical question, sorry if it's off topic. I am trying to understand the deviance returned by DESeq2. Could not find an explicit description so I assumed it would be the deviance of the fitted model compared to the saturated model, which is also what standard GLM functions ...
deseq2 written 20 days ago by Peter Langfelder1.7k • updated 20 days ago by Michael Love22k
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Comment: C: Rgraphviz installation fails in R with OpenBLAS
... Apologies for this late reply, I missed your question. The compiler was the same, gcc 8 (currently at version 8.2.1 but 3 months ago the version may have been a bit lower). It is likely that one had -O2 and the other -O3 because, upon re-installation of plain R with -O3 compiler setting (which propa ...
written 21 days ago by Peter Langfelder1.7k
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Comment: C: Taking into account strong batch effect in microarray differential expression an
... You can either run the data separately for each cell line or use the combined factor and contrasts approach. They should give you very similar scatterplots. The combined factor and contrast approach is perhaps somewhat preferable because the empirical Bayes moderation should have more samples to wor ...
written 26 days ago by Peter Langfelder1.7k
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Answer: A: Taking into account strong batch effect in microarray differential expression an
... The MDS/PCA plots just tell you that the effect of cell line is much greater than the effect of the perturbation. They don't tell you whether the effects of the perturbation are similar across the cell lines. I'd run limma on each cell line separately, then create scatterplots of the fold changes (c ...
written 27 days ago by Peter Langfelder1.7k
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Comment: C: Odd P-value distribution in edgeR on RRBS data
... I am not going to disagree with Gordon since he knows infinitely more than I do about the internal workings of the empirical Bayes moderation, but I have a comment on Aaron's code. When filtering by deviance, one needs to calculate the deviance from the fit to design ~1 (which is analogous to calcu ...
written 6 weeks ago by Peter Langfelder1.7k

Latest awards to Peter Langfelder

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 3 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Guru 9 months ago, received more than 100 upvotes.
Scholar 20 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 20 months ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
Scholar 20 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 20 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 20 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 20 months ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 20 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 2.0 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 3.0 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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