Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

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Answer: A: Information regarding the (minimum) number of genes needed to analyse with DESeq
... There are two primary concerns when analyzing a smaller number of genes. The first question is whether you have enough genes to estimate a robust dispersion trend. I think 380 genes should suffice for this. The second question is whether your targeted set of genes satisfies the criteria for the norm ...
written 5 days ago by Ryan C. Thompson6.5k
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Comment: C: How to write a preprocess.reads function for summarizeOverlaps that requires dif
... Ok, good to know. So basically, my preprocessing function should be prepared to handle any one of GAlignments, GAlignmentPairs, and GAlignmentsList. And furthermore it should be prepared to distinguish between mated and un-mated reads within a GAlignmentsList. ...
written 6 days ago by Ryan C. Thompson6.5k
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Comment: C: Limma model for paired and pool together
... I'm not sure I follow the logic that there's no heteroskedasticity issue. I would expect the pooled samples to have smaller residuals on average, although perhaps multiple pools would be required to show this effect. ...
written 6 days ago by Ryan C. Thompson6.5k
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Answer: A: Limma model for paired and pool together
... The main problem I see is that the pooled samples would be expected to have lower biological variance, since they are effectively the average of several donors. You can model this sample heteroskedasticity using a design of ~Cell + Donor and then using voomWithQualityWeights. Make sure to set plot=T ...
written 6 days ago by Ryan C. Thompson6.5k
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Comment: C: read counts for gene families
... Thanks for the correction. I've done most of my gene set testing with limma, so I'm less familiar with the options for edgeR. ...
written 9 days ago by Ryan C. Thompson6.5k
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Answer: A: read counts for gene families
... Generally I wouldn't recommend trying to combine counts from multiple different genes. What precisely is your null hypothesis? If you want to know whether any genes in a family are differentially expressed, you can use roast fry. If you want to know whether a family is enriched for differentially ex ...
written 9 days ago by Ryan C. Thompson6.5k
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Answer: A: normalisation of count data
... If you were fitting a linear model, the log fold changes would be identical. However, in a negative binomial GLM, the calculation of log fold changes depends on the estimated dispersion parameter, which depends on other genes. You might consider subsetting your genes after dispersion estimation, whi ...
written 11 days ago by Ryan C. Thompson6.5k
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How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
... I want to write a function that I can use as the preprocess.reads argument to summarizeOverlaps that will reduce each read to just the midpoint of the fragment represented by the read. For paired-end reads, this involves taking the midpoint of the outer ends of the two reads, while for single-end re ...
genomicalignments summarizeoverlaps written 12 days ago by Ryan C. Thompson6.5k • updated 11 days ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
... As far as I know, there is no separate function for this. Simply split or filter your results based on the sign of the logFC column. ...
written 13 days ago by Ryan C. Thompson6.5k
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Answer: A: Repeated Measures, Within-Subject, Between-Groups RNAseq Analysis
... For Question 1, the two designs are equivalent, and you should use whichever one you find more convenient. For Question 2, I would go with your first design, ~0+Group+Participant. The second design you suggest would fit a separate group effect for every participant, which you have stated is not you ...
written 15 days ago by Ryan C. Thompson6.5k

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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 11 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Scholar 11 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 13 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 13 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 13 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 14 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 24 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Scholar 24 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: DESeq2 how to define my conditions when I want the results comparing a subset of
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: edger, trended or common dispersion
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm

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