Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

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Answer: A: Filtering, minimum sample number, and condition in edgeR
... If you have many genes with many counts in one library and zero counts in all the replicates of that library, the first thing you should check is whether the outlier is the same library for all of these genes. If so, you may simply have a poor-quality library that consistently diverges from its repl ...
written 15 days ago by Ryan C. Thompson ♦ 7.1k
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Comment: C: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
... Hmm, it's been a while since I've actually chased down these references. Perhaps one of the limma authors more familiar with it can help? ...
written 4 weeks ago by Ryan C. Thompson ♦ 7.1k
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Answer: A: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
... The limma package has a function called genas that is meant to solve exactly this problem: estimating the degree of genuine correlation between fold changes that are expected to be correlated under the null hypothesis as a result of using a common reference. You should check into that function and t ...
written 4 weeks ago by Ryan C. Thompson ♦ 7.1k
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Answer: A: What is colData? How do I make one?
... The DESeqDataSet used by DESeq2 is a subclass of SummarizedExperiment, which is what provides rowData and colData. You should read more about SummarizedExperiment objects here: https://www.bioconductor.org/packages/devel/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html Briefly ...
written 4 weeks ago by Ryan C. Thompson ♦ 7.1k
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Answer: A: [Deseq2] Estimating size factors using samples which have been excluded for QC
... If you have samples that have failed QC, I would be careful about including them in the normalization. Presumably they failed QC because they have an abnormal distribution of read counts, so normalizing them against normal samples might not make sense. The main concern I would have is that the faile ...
written 5 weeks ago by Ryan C. Thompson ♦ 7.1k
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Answer: A: Finding DE genes from RNA-seq data
... You seem to have some of misconceptions about how differential expression testing works. First of all, changing the base used in the logarithm does not change the p-values. If you used base e or base 10, the logFC, logFPKM, and logCPM values would be different, but the p-values would still be identi ...
written 7 weeks ago by Ryan C. Thompson ♦ 7.1k
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Is it ok to use decideTests on linearly dependent contrasts?
... I have an RNA-seq experiment with 4 time points, and I would like to identify genes that change significantly in one direction and then later change significantly in the other direction (broadly speaking, I'm looking to distinguish between genes that change transiently and genes whose change is main ...
limma decidetests written 7 weeks ago by Ryan C. Thompson ♦ 7.1k • updated 7 weeks ago by Gordon Smyth ♦ 35k
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Comment: C: Dispersion fit and p-value distributions
... Also, to expand on why Bernd's recommendation to use the local dispersion fit rather than fdrtool is the correct one: solving the root cause of a bias is nearly always preferable to accepting the bias and then trying to model it later in the analysis, which is what fdrtool does. If you were unable t ...
written 8 weeks ago by Ryan C. Thompson ♦ 7.1k
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Comment: C: Dispersion fit and p-value distributions
... Oh, that's a good point. If that's the case, using the local dispersion fit is definitely the best solution. ...
written 8 weeks ago by Ryan C. Thompson ♦ 7.1k
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Answer: A: Dispersion fit and p-value distributions
... There's a couple of interesting things going on in your data. First of all, Groups 2 and 3 are clearly the 2 groups that are closest to each other (based on the PCA plot), so fewer differentially expressed genes are expected for this contrast. However, all groups appear to have roughly equal varianc ...
written 8 weeks ago by Ryan C. Thompson ♦ 7.1k

Latest awards to Ryan C. Thompson

Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Finding DE genes from RNA-seq data
Popular Question 6 weeks ago, created a question with more than 1,000 views. For summarizeOverlaps using GRanges or bed file as reads?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Voom transformation from counts and normalization to negative values
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Voom transformation from counts and normalization to negative values
Appreciated 3 months ago, created a post with more than 5 votes. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 6 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Popular Question 6 months ago, created a question with more than 1,000 views. For edgeR Quasi-likelihood with tagwise dispersion?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 6 months ago, created a question with more than 1,000 views. For summarizeOverlaps using GRanges or bed file as reads?
Scholar 7 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 17 months ago, created an answer that has been accepted. For A: How does the function model.matrix (to define experimental design) really works
Scholar 17 months ago, created an answer that has been accepted. For A: Duplicate Correlation with technical replicates
Scholar 17 months ago, created an answer that has been accepted. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How does the function model.matrix (to define experimental design) really works
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 17 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Appreciated 17 months ago, created a post with more than 5 votes. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: edger glmQLFit mix glmLRT
Popular Question 17 months ago, created a question with more than 1,000 views. For Rsubread::featureCounts extremely slow on some annotations
Student 17 months ago, asked a question with at least 3 up-votes. For Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
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