Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 634 results • page 1 of 64 • next >
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Answer: A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
... Leaving in the 3rd group should make barely any difference in the normalization step. In the absence of large global changes in expression, normalization relationships between samples should be approximately transitive, so adding a third group should not substantially change the relative normalizati ...
written 1 day ago by Ryan C. Thompson5.4k
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Comment: C: limma and edgeR QL strange results
... That look correct, except that I'm not sure where you're getting the "contrast.matrix" function. The function I know of is "makeContrasts", which works a little differently (read the help text). ...
written 6 days ago by Ryan C. Thompson5.4k
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Comment: C: limma and edgeR QL strange results
... There's no need for it, since it will fit exactly the same model and give identical results. But you would just use a formula of ~ sex * condition. Then you would stare at the contents of the design matrix while ignoring the possibly misleading column names until you understand what the coefficients ...
written 7 days ago by Ryan C. Thompson5.4k
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Comment: C: limma and edgeR QL strange results
... When building a design matrix, I always recommend avoiding factorial designs if at all possible. In my experience teaching this to people, the factorial design is the least intuitive way to parametrize the design, and oftencauses people to misinterpret coefficients based on the misleading names give ...
written 7 days ago by Ryan C. Thompson5.4k
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Comment: C: limma and edgeR QL strange results
... No, it's not the same. Condition is not nested within sex, while subject is. (In the edgeR example, hormone is not nested within disease while patient is.) The nesting affects what kind of contrasts you can test and how you must specify them. ...
written 7 days ago by Ryan C. Thompson5.4k
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Comment: C: limma and edgeR QL strange results
... Using that method of constructing the design matrix, and assuming the factors levels are alphabetical, you should have a "sexM" coefficient in your design matrix, which represents the difference between the first female and the first male subjects. Note that the code in section 3.5 of the edgeR user ...
written 7 days ago by Ryan C. Thompson5.4k
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Answer: A: limma and edgeR QL strange results
... The third dimension of your MDS plot is indeed showing a significant difference between males and females, but this does not imply an interaction between the effects for sex and condition. From everything you've shown, it looks to me that the interaction effect is negligible for most genes. You can ...
written 7 days ago by Ryan C. Thompson5.4k
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Answer: C: How to interpret plotBCV plots in edgeR
... That is indeed a highly suspect BCV plot, and I would probably not trust the results of a differential expression test on this data until you figure out what is causing this. Can you provide the code, design matrix, and/or data that you used to generate this plot? Also, can you please show the MDS p ...
written 7 days ago by Ryan C. Thompson5.4k
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Answer: A: Comparing across sets of regulated genes -- Strategies?
... There are lots of options for getting at your questions. Here are a few of them: For your third question, regarding the overall similarity of the logFC values across all genes in two contrasts, there's a function in limma called genas that can do that. It will give you the estimate of biological co ...
written 7 days ago by Ryan C. Thompson5.4k
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Comment: C: DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq
... Both edgeR and DESeq2 can handle any valid design matrix and contrast. However, you don't need to switch your differential expression testing to edgeR just to use the cpm function. You just need to create a DGEList, run calcNormFactors (with method="RLE" to be consistent with DESeq2), and then run c ...
written 9 days ago by Ryan C. Thompson5.4k

Latest awards to Ryan C. Thompson

Teacher 1 day 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: edger, trended or common dispersion
Scholar 10 months ago, created an answer that has been accepted. For A: Adjusting for confounders along with paired testing using edgeR
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: FDR and padj in deseq and edger
Teacher 10 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
Scholar 10 months ago, created an answer that has been accepted. For A: Technical and biological replates in BitSeq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Low percentage of assigned fragments with FeatureCounts
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: On the relationship between design and contrasts
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Scholar 10 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Scholar 10 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to use removeBatchEffect for removing effect of multiple confounding variabl
Scholar 10 months ago, created an answer that has been accepted. For A: edgeR RNA-seq analysis using glm
Scholar 10 months ago, created an answer that has been accepted. For A: Duplicate Correlation with technical replicates
Scholar 10 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Using multiple tools for differential gene expression analysis as validation
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: How to remove dublicate probesets matching to the same gene, after toptable in o
Scholar 10 months ago, created an answer that has been accepted. For A: ribosome profiling analysis with different dispersions

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