User: bkellman

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Posts by bkellman

<prev • 17 results • page 1 of 2 • next >
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Comment: C: DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
... @Michael Love, I know this is an appropriate solution in the context of the history of statistics, but I've gotten frequent concern from Biologists when suggesting they use this approach (rather than gene list overlap). Do you have any papers you like to point to to make Biologists a little more com ...
written 2.0 years ago by bkellman0
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Comment: C: Estimating group-specific dispersion in DESeq2
... I ran a quick preliminary check. It looks like the correlation of dispersions diverges quickly when the min rowSums is raised from 1,10,100 (for 100 samples: 70 ASD, 30 TD). So for genes with a base mean > 1 there is little cohesion between the separate assessments. Let me get an example gene. ...
written 2.7 years ago by bkellman0
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Comment: C: Estimation of dispersion in DeSeq and DeSeq2
... Thanks! Let me repost this. I think this is a useful exchange and I need some clarification https://support.bioconductor.org/p/89105/ ...
written 2.7 years ago by bkellman0
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Estimating group-specific dispersion in DESeq2
... Is there a reason that the 'per-sample' dispersion calculation was discontinued for DESeq2? I am working with ASD samples which have been observed [ http://dx.doi.org/10.1371/journal.pone.0016715 ] to exhibit lower variance. I need to estimate the ASD and typical dispersion separately. Can I do this ...
deseq deseq2 estimatedispersions written 2.7 years ago by bkellman0 • updated 2.7 years ago by Michael Love24k
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Comment: C: Estimation of dispersion in DeSeq and DeSeq2
... Thanks! Let me repost this. I think this is a useful exchange and I need some clarification ...
written 2.7 years ago by bkellman0
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Comment: C: Estimation of dispersion in DeSeq and DeSeq2
... Michael, Is there a reason that the per-sample dispersion calculation was discontinued for DESeq2? I am working with ASD samples which have been observed [ http://dx.doi.org/10.1371/journal.pone.0016715 ] to exhibit lower variance. I need to estimate the ASD and typical dispersion separately. Can I ...
written 2.7 years ago by bkellman0
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Comment: C: Coping with a label/class imbalance in DESeq2
... I see what you are saying, I do think that speed of convergence could be an issue. Though I don't have an intuition about what scale of class imbalance would be necessary to see a significant difference in convergence speeds.  I think I have found code (line 317, DESeq.cpp) that gets at the root of ...
written 2.8 years ago by bkellman0
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Comment: C: Coping with a label/class imbalance in DESeq2
... I have had concerns about the assumption of consistent variance within each gene across groups but over time I've come to accept it as respectably conservative. ...
written 2.8 years ago by bkellman0
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Comment: C: Coping with a label/class imbalance in DESeq2
... This is an interesting insight. I haven't heard the term "noise floor" before. Where is that from? ...
written 2.8 years ago by bkellman0
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Comment: C: Coping with a label/class imbalance in DESeq2
... Great! I have no empirical means to disagreeing. But I am still stuck on the theory. In the Github repo, line 2018-2020 of core.R says: mu <- normalizationFactors * t(exp(modelMatrix %*% t(betaRes$beta_mat))) # establish library adjusted betas (I assume?) logLike <- nbi ...
written 2.8 years ago by bkellman0

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