Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 652 results • page 1 of 66 • next >
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Comment: C: Calculating probability of getting xx genes past FDR10%
... This is not a Bioconductor question. You should familiarize yourself with the definition of false discovery rate, because you are misunderstanding it here.   ...
written 1 day ago by Ryan C. Thompson5.6k
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Answer: A: Is there any point to TMM-normalize TPM prior to limma-voom?
... tximport should always giving you a matrix of values on a raw count scale. The only difference is whether it takes the estimated counts reported directly by Kallisto or whether it starts from the TPM values and transforms them back to counts. So either way you have a count matrix, not a TPM matrix. ...
written 1 day ago by Ryan C. Thompson5.6k
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Answer: A: limma blocking and including covariates
... Whatever you choose to do, you should only adjust for inter-patient differences once in your design. If all your covariates only vary by patient, then I believe including them in the design is redundant with blocking on patient using duplicateCorrelation, since blocking on patient already adjusts fo ...
written 2 days ago by Ryan C. Thompson5.6k
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Answer: A: DESeq2 input- normalized counts that were processed
... I'm not sure what the point of scaling all the counts in a sample is. If you're subtracting the same percent from every gene's count for a given sample, it will have no net effect on the fold change calculations, since the size factors will undo this scaling. The only effect will be to make the disp ...
written 7 days ago by Ryan C. Thompson5.6k
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Comment: C: DESeq2 model design with unequal number of time points
... One more thing I should mention: I believe DESeq2 automatically sets betaPrior=FALSE for interaction models. Since this is definitely an interaction model, you should set betaPrior=FALSE manually, since there's no way for DESeq2 to know that it's an interaction model when you concatenate the two fac ...
written 12 days ago by Ryan C. Thompson5.6k
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Answer: A: DESeq2 model design with unequal number of time points
... Yes, the reason this is happening is because of the missing/mismatched time points. As you point out, when working directly with a design matrix, you can manually remove the columns of all zeros and still get a functional design matrix, although I haven't tried this in a design with interaction term ...
written 14 days ago by Ryan C. Thompson5.6k
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Comment: C: edgeR ANOVA-like analysis
... No, for N groups, you require N-1 contrasts to do an ANODEV test. Pick one group arbitrarily and form contrasts of every other group against that one. (It doesn't matter which one you pick, you'll get the same p-values.) ...
written 14 days ago by Ryan C. Thompson5.6k
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Answer: A: bias correction (an example from ChIP-seq)
... You should read through the normalization section of the csaw User's Guide. It gives a fairly in-depth discussion of normalization issues for ChIP-Seq data. I'm not exactly sure how you're defining a "gene" for ChIP-Seq data, which can detect binding anywhere in the genome, not just in gene bodies o ...
written 15 days ago by Ryan C. Thompson5.6k
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Answer: A: LIMMA paired analysis adjusting for two continuous variables - microarray data
... It sounds like you basically want to treat age and BMI as confounding factors and control for their influence, and you're not interested in the genes that are differentially expressed with respect to either one. If so, the design you probably want is just design <- model.matrix(~class + ID) Th ...
written 20 days ago by Ryan C. Thompson5.6k
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Comment: C: Edge R Issue from a basic differential expression analysis
... I'm not telling what you should be using, I'm telling you what you are currently using. The voom, lmFit, eBayes, and topTable functions are all part of limma, not edgeR, as you can see from reading the help pages for those functions. If this is the analysis pipeline you are using, you should tag you ...
written 22 days ago by Ryan C. Thompson5.6k

Latest awards to Ryan C. Thompson

Teacher 15 days ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 15 days ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 28 days ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 28 days ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 4 weeks ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 5 weeks 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: DESeq2 how to define my conditions when I want the results comparing a subset of
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Scholar 11 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Scholar 11 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: edger, trended or common dispersion
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm
Good Answer 11 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 11 months ago, created an answer with at least 3 up-votes. For A: On 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 11 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
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: Duplicate Correlation with technical replicates

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