Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 790 results • page 2 of 79 • next >
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Comment: C: unexpected p-value histogram in edgeR
... Sorry, I think I explained poorly. I didn't mean that different contrasts could have different BCV values. I meant that if one contrast involves only samples in the data set with lower-than-average variability, then the null distribution of logFC values will be smaller than expected for the whole-da ...
written 12 weeks ago by Ryan C. Thompson6.8k
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Comment: C: unexpected p-value histogram in edgeR
... I have seen the type of p-value distribution that you are seeing in similar situations. Specifically, when a particular contrast has both little to no real differential expression and low biological variability relative to other contrasts in the same data set. The result is that the null distributio ...
written 12 weeks ago by Ryan C. Thompson6.8k
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Answer: A: DESseq2: Why can the dispersion be generelized over the conditions?
... The core issue is that if you want to estimate more parameters (such as additional dispersions for each group), you need more data. DESeq2 shares dispersion information between genes to make up for the fact that the data for a single gene is already insufficient to yield a stable estimate of even a ...
written 3 months ago by Ryan C. Thompson6.8k
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Comment: C: DESeq Timepoint Design (using Baseline as reference)
... Are you trying to identify specific genes that have different response in the two conditions, or are you just trying to determine whether the two gene signatures are distinct? ...
written 3 months ago by Ryan C. Thompson6.8k
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Comment: C: How to get the ordinary t statistic for two paired groups?
... Oh, sorry, I didn't notice that detail. Please disregard my answer. ...
written 3 months ago by Ryan C. Thompson6.8k
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Answer: A: How to get the ordinary t statistic for two paired groups?
... I believe the default for t.test is to assume unequal group variances, while limma assumes equal variances. I'm not sure how much of a discrepancy you are seeing, but this might explain the difference. ...
written 3 months ago by Ryan C. Thompson6.8k
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Comment: C: How to obtain a normalised expression matrix from read counts and scaling factor
... It would be easiest if you used the DGEList class to contain both the counts and normalization factors. For example: dge <- DGEList(matrix) dge_tmm <- calcNormFactors(dge, method="TMM") cpm(dge_tmm) ...
written 4 months ago by Ryan C. Thompson6.8k
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Answer: A: How to obtain a normalised expression matrix from read counts and scaling factor
... There's no need to work out the correct formula for yourself. This is already implemented in the cpm function. You simply need to pass the count matrix and normalization factors as the correct arguments. Please read the help text for this function. ...
written 4 months ago by Ryan C. Thompson6.8k
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Comment: C: Calling svaseq() multiple times
... I don't believe that sva is an algorithm that can "converge". You can keep adding additional surrogate variables until they eat up all the residual variation and your model has as many coefficients as you have samples, at which point you can no longer fit the model at all. Like I said, you can let s ...
written 4 months ago by Ryan C. Thompson6.8k
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Answer: A: Calling svaseq() multiple times
... What is your goal in running sva multiple times? Are you just trying to estimate additional surrogate variables? SVA tries to estimate the appropriate number of surrogate variables, but If you want more surrogate variables, you can simply override its decision by setting n.sv. I'm not aware of any r ...
written 4 months ago by Ryan C. Thompson6.8k

Latest awards to Ryan C. Thompson

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 3 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 3 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Popular Question 3 months ago, created a question with more than 1,000 views. For edgeR Quasi-likelihood with tagwise dispersion?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 3 months ago, created a question with more than 1,000 views. For summarizeOverlaps using GRanges or bed file as reads?
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: What's the relationship between "design" and "contrasts"?
Scholar 15 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 15 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 15 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 15 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 15 months ago, created an answer that has been accepted. For A: Duplicate Correlation with technical replicates
Scholar 15 months ago, created an answer that has been accepted. For A: How does the function model.matrix (to define experimental design) really works
Scholar 15 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Batch correction in DESeq2
Popular Question 15 months ago, created a question with more than 1,000 views. For Low-count filtering with uneven sequencing depth between samples?
Popular Question 15 months ago, created a question with more than 1,000 views. For Rsubread::featureCounts extremely slow on some annotations
Popular Question 15 months ago, created a question with more than 1,000 views. For Missing as.list generic from AnnotationDbi?
Popular Question 15 months ago, created a question with more than 1,000 views. For Equivalent of contrasts.fit & multi-contrast decideTests for edgeR?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: edger glmQLFit mix glmLRT
Scholar 15 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: ribosome profiling analysis with different dispersions

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