Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 795 results • page 1 of 80 • next >
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Comment: C: DEseq2 - minimum number of genes
... Adding fake data isn't going to solve anything, it's just going to make the data worse. If you do so, you'll effectively be making an arbitrary determination of the size factors with no evidence while also disrupting the dispersion estimation. ...
written 5 days ago by Ryan C. Thompson6.9k
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Comment: C: DESeq2 normalization Factor Matrix to correct for uneven targeted sequencing cov
... Are you sure it makes sense to run DESeq2 on this data? Isn't this data better suited to fitting a logistic regression model for each mutation? ...
written 13 days ago by Ryan C. Thompson6.9k
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Comment: C: Batch correction when only some subjects have replicates across batches
... One thing that just occurred to me is that it might be possible to use voomWithQualityWeights to determine whether there is a data issue to begin with. Run it on the full data set with a design of ~ patient + time + batch, and then compare the weights of the shared samples against the non-shared one ...
written 18 days ago by Ryan C. Thompson6.9k
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Comment: C: Batch correction when only some subjects have replicates across batches
... Perhaps using arrayWeights with a var.design that separates the samples into cross-batch controls and everything else? ...
written 19 days ago by Ryan C. Thompson6.9k
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Comment: C: Batch correction when only some subjects have replicates across batches
... If I understand correctly, your design is a bit different than the question you reference, because your samples shared across batches are effectively technical replicates, i.e. the same biological sample sequenced in each batch, as opposed to different biological replicates in the same treatment gro ...
written 20 days ago by Ryan C. Thompson6.9k
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Comment: C: Voom transformation from counts and normalization to negative values
... logCPM values are what they sound like: the logarithm (in base 2) of the counts for that gene divided by the total millions of counts. This normalizes for differences in sequencing depth between samples and nothing else. If you don't provide any further information, that's exactly what you get. If y ...
written 22 days ago by Ryan C. Thompson6.9k
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Comment: C: Voom transformation from counts and normalization to negative values
... The use of voom in the context of that question is extraneous. The function is calling voom and then throwing away the weights that it calculated, keeping only the logCPM values. If all you want is the logCPM values, then use the cpm function as I've described in my answer. Looking at the other cod ...
written 22 days ago by Ryan C. Thompson6.9k
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Comment: C: Voom transformation from counts and normalization to negative values
... This is also documented in the help page. See the appropriately-named normalize.method argument. The default is "none", which performs no additional normalization after the logCPM transformation. ...
written 22 days ago by Ryan C. Thompson6.9k
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Answer: A: Voom transformation from counts and normalization to negative values
... The voom function computes logCPM values using whatever normalization information you choose to provide. This is documented in the help page for voom. Generally, you should be running it on a DGEList object after running calcNormFactors on the DGEList. See the help page for calcNormFactors if you wa ...
written 22 days ago by Ryan C. Thompson6.9k
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Answer: A: Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
... There are trade-offs to both approaches. If you fit a separate model for every gene, you lose the core feature of limma: empirical Bayes information sharing when estimating the variance for each gene. The other main difference is that limma's mixed model functionality estimates a single correlation ...
written 27 days ago by Ryan C. Thompson6.9k

Latest awards to Ryan C. Thompson

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Voom transformation from counts and normalization to negative values
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 4 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 4 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 4 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 4 months ago, created a question with more than 1,000 views. For summarizeOverlaps using GRanges or bed file as reads?
Popular Question 4 months ago, created a question with more than 1,000 views. For edgeR Quasi-likelihood with tagwise dispersion?
Scholar 5 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 16 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 16 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
Scholar 16 months ago, created an answer that has been accepted. For A: Duplicate Correlation with technical replicates
Scholar 16 months ago, created an answer that has been accepted. For A: How does the function model.matrix (to define experimental design) really works
Teacher 16 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 16 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 16 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Popular Question 16 months ago, created a question with more than 1,000 views. For Rsubread::featureCounts extremely slow on some annotations
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Batch correction in DESeq2
Popular Question 16 months ago, created a question with more than 1,000 views. For Low-count filtering with uneven sequencing depth between samples?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: edger glmQLFit mix glmLRT
Popular Question 16 months ago, created a question with more than 1,000 views. For Missing as.list generic from AnnotationDbi?
Popular Question 16 months ago, created a question with more than 1,000 views. For Equivalent of contrasts.fit & multi-contrast decideTests for edgeR?

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