Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 731 results • page 2 of 74 • next >
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Help running the nondetects::qpcrImpute on my data?
... I am trying to run the qpcrImpute function from the nondetects package on my qPCR data, and I am running into some issues. After some experimentation, I have formatted my data with one row per gene, with each technical replicate in a separate column, which seems to match the format of the data in th ...
software error nondetects written 4 weeks ago by Ryan C. Thompson6.3k • updated 4 weeks ago by valery.sherina10
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Comment: C: Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
... Would the QL pipeline actually use the computed robustness weights, or would it just use the dispersion trend that was estimated robustly but ignore the weights themselves? ...
written 9 weeks ago by Ryan C. Thompson6.3k
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Comment: C: DESeq2 Different Results when using different foreach parallel backends
... Maybe biocparallel should have an option and/or default to use doRNG? https://cran.r-project.org/web/packages/doRNG/index.html ...
written 10 weeks ago by Ryan C. Thompson6.3k
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Comment: C: glmTreat Errors for multi coefficient and analysis of deviance situations.
... Just to give a few other possible ways to define the null hypothesis for multi-coefficient treat that make equal sense, consider: |c| + |s| < threshold, or c^2 + s^2 < threshold^2. Of course, all of these are still dependent on the parametrization. ...
written 10 weeks ago by Ryan C. Thompson6.3k
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Comment: C: glmTreat Errors for multi coefficient and analysis of deviance situations.
... The problem with that is that the region defined by your null hypothesis is now dependent on how you've parametrized your design matrix in ways that are probably not intuitive. That is, tests using different design matrices that would be equivalent in glmLRT or glmQLFTest would give different result ...
written 10 weeks ago by Ryan C. Thompson6.3k
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Answer: A: glmTreat Errors for multi coefficient and analysis of deviance situations.
... As far as I know, the treat method is only defined for a single coefficient or contrast at a time. I'm not even sure what the null hypothesis would be for testing multiple coefficients at once. ...
written 10 weeks ago by Ryan C. Thompson6.3k
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
... If you haven't already, you should check out the csaw package, both the User's Guide and the associated publication. ...
written 10 weeks ago by Ryan C. Thompson6.3k
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Comment: C: Loads, really loads of DEGs after edgeR differential analysis
... I know edgeR::estimateDisp definitely works with R 3.4.2. Perhaps the locfit package or some other dependency needs to be reinstalled after updating R? To answer your question about normalization, you should read the paper on TMM, the default edgeR normlization, and have a look at the help page for ...
written 11 weeks ago by Ryan C. Thompson6.3k
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Comment: C: Effect of lfcThreshold on p-value in DESeq2
... Yes, you've understood correctly. There is a lot of bad advice out there, and one of the most common bits of bad advice is filtering based on fold change separately from significance testing. If you filter fold changes in this way, the FDR estimation has no knowledge of your fold change filtering cr ...
written 11 weeks ago by Ryan C. Thompson6.3k
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Answer: A: Loads, really loads of DEGs after edgeR differential analysis
... Based on the clarifications in your comments, a few things are clear. First, you are using the old dispersion estimation pipeline. I recommend that you switch to using the newer estimateDisp function, which estimates the common, trended, and tagwise dispersions all in one, and runs faster as well. T ...
written 11 weeks ago by Ryan C. Thompson6.3k

Latest awards to Ryan C. Thompson

Teacher 8 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"?
Popular Question 9 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Scholar 9 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"?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
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"?
Scholar 11 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 11 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 11 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 22 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Scholar 22 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Teacher 22 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 22 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: edger, trended or common dispersion
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm

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