Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

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Comment: C: DESeq2: dealing with outliers
... Perhaps plotCounts should plot replaced counts using a different color or shape to make it more obvious which counts have been replaced. ...
written 3 days ago by Ryan C. Thompson ♦ 5.8k
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Answer: A: Limma validity for only hundreds of genes/metabolites
... I think I recall an instance where Gordon said that the empirical Bayes squeezing employed by limma could theoretically work with as few as 4 genes. I believe a few hundred should be fine. ...
written 7 days ago by Ryan C. Thompson ♦ 5.8k
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Answer: A: How to adjust for different cell type mixtures in differential expression analys
... By my understanding, one problem with putting the cell type compositions directly into the model as numeric covariates is the incompatible scales: that cell fractions are expected to have a linear relationship to gene abundance, while model coefficients are fit on a log scale. You might be better of ...
written 9 days ago by Ryan C. Thompson ♦ 5.8k
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Answer: A: Filtering DGEList object in edgeR
... If you want to add additional gene metadata, do so by adding columns to the d$genes data frame (or creating it if it doesn't exist). Similarly, to add sample metadata, add columns to the d$samples data frame. These elements will be subset along with the counts matrix as you expect. ...
written 17 days ago by Ryan C. Thompson ♦ 5.8k
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Answer: A: differentially expressed genes without contrasts
... If one of your model coefficients already corresponds to the hypothesis you want to test, then you do not need a contrast. Otherwise, the purpose of contrasts is to express the linear combination of coefficients that represents your hypothesis. ...
written 19 days ago by Ryan C. Thompson ♦ 5.8k
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Comment: C: pvalue of deseq2
... When you posted this question, you misspelled the metaseq tag. I've fixed the spelling, which should improve the chances that the authors of that package will see it. ...
written 20 days ago by Ryan C. Thompson ♦ 5.8k
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Comment: C: pvalue of deseq2
... I'm not familiar with the metaseq package, so I can't tell you how to use it with DESeq2, but if all it needs is a vector of p-values for each gene, DESeq2 can certainly provide that. If you want to know how to use DESeq2 in general, it comes with a detailed manual. ...
written 20 days ago by Ryan C. Thompson ♦ 5.8k
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Answer: A: pvalue of deseq2
... The normalization options are not for normalizing the p-values, they are for normalizing the RNA-seq data that is input into NOISeq. This option is not needed for DESeq2 or edgeR because both methods already implement their own normalizations. In fact, TMM is the edgeR normalization method. So if yo ...
written 20 days ago by Ryan C. Thompson ♦ 5.8k
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Comment: C: pvalue of deseq2
... You're going to have to explain what you mean by normalizing p-values. Are you talking about corrections for multiple testing? ...
written 20 days ago by Ryan C. Thompson ♦ 5.8k
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Answer: A: RNAseq with technical replicates: Does it sound right?
... Yes, that's generally correct. The trick is that technical variation in count data, in the absence of any other substantial biases or technical effects, is approximately Poisson distributed, and the sum of independent Poisson-distributed variables (i.e. the counts for the same gene in multiple lanes ...
written 29 days ago by Ryan C. Thompson ♦ 5.8k

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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
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Popular Question 8 weeks ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
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Teacher 4 months 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: What's the relationship between "design" and "contrasts"?
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Scholar 4 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Appreciated 4 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
Scholar 4 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 4 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
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Scholar 15 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
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