User: Homer

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Homer0
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Posts by Homer

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Comment: C: Comparison of DESeq2 and BNB-R model
... Thanks for your quick reply. And sorry, maybe I have to clarify my thoughts a bit. In DESeq2, the variance of the negative binomial distribution of a count `K_ij` (with `i` indexing the gene and `j` the sample) is `Var(K_ij) = mu_ij + alpha_i * mu_ij^2 = s_j * exp(x_j^T * beta_i) + alpha_i * (s_j * ...
written 10 weeks ago by Homer0
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Comparison of DESeq2 and BNB-R model
... Hi, I am trying to understand and compare the DESeq2 model and the BNB-R (https://github.com/siamakz/BNBR) model. The corresponding references are: - DESeq2: Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genom ...
deseq2 bnb-r written 10 weeks ago by Homer0 • updated 10 weeks ago by Michael Love22k
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DESeq2/apeglm s-values: Why average FSR (or FSOS) instead of maximum?
... I have a methodical question concerning the s-values computed by DESeq2::lfcShrink() using the apeglm shrinkage option: Why did you decide to calculate the average instead of the maximum of the local false sign rate (local FSR) of all genes which have a local FSR smaller than or equal to the local F ...
deseq2 written 5 months ago by Homer0 • updated 5 months ago by Michael Love22k

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