Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... The untranslated regions are part of the same mRNA molecule as the CDS. Why would you want to ignore them? You would just be throwing away information about the mRNA abundance. ...
written 5 weeks ago by Ryan C. Thompson6.1k
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Comment: C: Why different filtering criteria using CPM to filter the RNA-seq count data in e
... If you search this help forum, you'll find lots of advice on how to filter RNA-seq data. There's no one threshold that's guaranteed to work for all data sets. ...
written 5 weeks ago by Ryan C. Thompson6.1k
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... Are you talking about measuring alternate splicing? What exactly are you trying to measure? ...
written 5 weeks ago by Ryan C. Thompson6.1k
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... Are you asking if it's OK to exclude the UTRs from the gene model when quantifying genes from reads? Why would you want to do this? ...
written 5 weeks ago by Ryan C. Thompson6.1k
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Answer: A: One-condition limma test
... Limma typically works with data on a log scale, so I think you would want to work with log ratios. If you take the log of your data, then your null hypothesis becomes logratio = 0. You can test this hypothesis by fitting an intercept-only model (i.e. ~1) and testing whether the sole coefficient is n ...
written 6 weeks ago by Ryan C. Thompson6.1k
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Answer: A: tximport recommendation for limma-trend downstream analysis?
... You can force cpm to use the offset matrix by passing exp(offset) as the library size. For cpm, I don't think this should make any difference relative to using lengthScaledTPM without offsets, so the only advantage is being able to use the same tximport run for edgeR, DESeq2, and limma. For voom, I ...
written 7 weeks ago by Ryan C. Thompson6.1k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... I think it is. If your design has 3 groups, A, B, and C, then a typical design matrix will have coefficients representing A, B-A, and C-A. In that case, if you want C-B, you need to make a contrast between the latter two coefs. I don't think that shrinking the B-A and C-A coefs will result in equiva ...
written 8 weeks ago by Ryan C. Thompson6.1k
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Comment: C: EdgeR: Replicate samples diverge in MDS plot
... I'm not sure. It might be possible. It depends on the severity of the confounding effect and the number of samples affected. sva and similar methods work best with lots of samples. ...
written 8 weeks ago by Ryan C. Thompson6.1k
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Answer: A: EdgeR: Replicate samples diverge in MDS plot
... It's impossible to know for sure with only 4 samples, but one possible explanation is that dimension 1 represents some sort of sample quality issue in the resistant2 sample that perturbed the measurements of gene expression in that sample, causing it to diverge from the others, while dimension 2 rep ...
written 8 weeks ago by Ryan C. Thompson6.1k
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Answer: A: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... From my perspective, one big issue with imposing a prior on log fold changes is that your model becomes dependent on your choice of parametrization. Alternate paratrizations of the same design are no longer equivalent. Effectively, in addition to specifying the model space, you now also need to spec ...
written 8 weeks ago by Ryan C. Thompson6.1k

Latest awards to Ryan C. Thompson

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 5 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 Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Scholar 6 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 19 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Scholar 19 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Teacher 19 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 19 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: edger, trended or common dispersion
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm

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