Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

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Answer: A: limma-trend with random effects and/or array weights
... The issues that occur when mixing voom with arrayWeights and/or duplicateCorrelation happen because the voom step comes before the arrayWeights or duplicateCorrelation steps, but in order to be fully accurate, the voom step needs information from those other steps. The solution implemented in voomWi ...
written 13 minutes ago by Ryan C. Thompson5.9k
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Comment: C: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
... Sounds good to me. ...
written 8 days ago by Ryan C. Thompson5.9k
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Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
... I have a BED file from an external data source that is tab-separated with spaces in the name field for some rows. These fields are not quoted. Looking at the code for rtracklayer::import.bed, it seems to use read.table with the default separator argument and no option to change it, which means all w ...
rtracklayer software error bed written 8 days ago by Ryan C. Thompson5.9k • updated 8 days ago by Michael Lawrence9.5k
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Comment: C: Why Differential expression results differ with edgeR and limma ?
... I'd say this is definitely an unexpected result. limma and edgeR generally have pretty good agreement on which genes are significant, and even when they don't, they should still give similar logFC and logCPM/AveExpr values. The fact that edgeR is reporting logFC values as high as 7 and limma is only ...
written 4 weeks ago by Ryan C. Thompson5.9k
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Answer: A: Prefering Grouping variables or Interaction terms in Experimental Design
... The one thing I've learned that's not obvious when you're first learning about design matrices is that two different design matrices can represent the same design. When using the likelihood ratio test and similar tests, combining genotype and time into a single "group" variable is equivalent to usin ...
written 5 weeks ago by Ryan C. Thompson5.9k
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Comment: C: LFDR PROPTRUENULL LIMMA
... To reiterate what I already said, propTrueNull is not telling you anything about significance. It is not telling you that 97.8% of your p-values are significant. If you want to select a subset of p-values with a specified false discovery rate, use p.adjust. ...
written 6 weeks ago by Ryan C. Thompson5.9k
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Answer: A: LFDR PROPTRUENULL LIMMA
... You've misunderstood the purpose of ptopTrueNull. propTrueNull does not give you information about specific hypothesis tests. It only estimates the overall proportion of tests whose null hypotheses are true. It does not give you a significance threshold. In your case, propTrueNull is estimating that ...
written 6 weeks ago by Ryan C. Thompson5.9k
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Answer: A: edgeR: How to set model for glmQLFTest in time-course experiment (compared to gl
... As far as I know, the quasi-likelihood F test supports all the same designs and contrasts as the LRT, and the usage is almost identical. Just swap out glmFit for glmQLFit and swap out glmLRT for glmQLFTest. If you're having a specific problem getting it to work, please update your question with deta ...
written 7 weeks ago by Ryan C. Thompson5.9k
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Answer: A: Exporting normalized counts over final DB windows from csaw
... Since csaw creates a DGEList and uses edgeR for the differential binding tests, you can just use the cpm function from edgeR to get the normalized counts-per-million values, which should be comparable between samples and between windows since all windows are the same size. You can attach the CPM val ...
written 7 weeks ago by Ryan C. Thompson5.9k
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Answer: A: Does LIMMA accept as an input "variance Stabilizing Transformation" generated by
... There is generally no reason to do this. You can either use voom before running limma or run eBayes with trend=TRUE. Either of these methods should give better results than using VST data. ...
written 8 weeks ago by Ryan C. Thompson5.9k

Latest awards to Ryan C. Thompson

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 4 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Scholar 4 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 4 months ago, created an answer with at least 3 up-votes. 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"?
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"?
Scholar 6 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 6 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 6 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 17 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Scholar 17 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Teacher 17 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 17 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: edger, trended or common dispersion
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm

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