User: Homer

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Homer0
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Posts by Homer

<prev • 10 results • page 1 of 1 • next >
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Comment: C: limma: parameter s0^2 for prior of residual variances
... Thank you for your answer that I understand in the way that the limma User's Guide is wrong. Your answer doesn't say that my formula for the prior mean of the `(sigma_g)^2` is wrong and the corrected version of the publication still contains the scaled inverse chi-squared distribution as the prior f ...
written 6 weeks ago by Homer0
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limma: parameter s0^2 for prior of residual variances
... The limma User's Guide says on p. 62 that the parameter `(s_0)^2` is the mean of the inverse chi-squared prior for the true residual variances `(sigma_g)^2`. However, if I get Smyth, G. K. (2004). Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experime ...
limma written 6 weeks ago by Homer0 • updated 6 weeks ago by Gordon Smyth39k
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edgeR default normalization method
... The help page for `edgeR::calcNormFactors()` says > The default method was changed from "TMM" to "TMMwsp" in the Bioconductor 3.9 release. However, I still get the results from the TMM method by default, not the TMMwsp method. Am I doing something wrong or is this a bug/error in the documentati ...
edger written 7 weeks ago by Homer0 • updated 7 weeks ago by Gordon Smyth39k
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Comment: C: DESeq2 s-value threshold for FSOS events
... Thanks a lot for your answer. I'll try to conduct a power/error analysis based on simulated data. ...
written 8 weeks ago by Homer0
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DESeq2 s-value threshold for FSOS events
... At different places (the help page for `DESeq2::plotMA()`, the apeglm vignette, and [here][1]) an s-value threshold of 0.01 or 0.005 is mentioned as a sensible choice for "false sign" (FS) events. However, when specifying a non-zero threshold for the log2 fold change in `DESeq2::lfcShrink()`, the re ...
deseq2 written 8 weeks ago by Homer0 • updated 8 weeks ago by Michael Love25k
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Answer: A: DESeq2 Wald test p-values
... Sorry, just realized my mistake: I was using a threshold for the log fold change. ...
written 8 weeks ago by Homer0
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DESeq2 Wald test p-values
... I don't understand how DESeq2 calculates the p-values given by `DESeq2::results()`. I thought it was 2 * pnorm(abs(log2FoldChange / lfcSE), lower.tail = FALSE) with `log2FoldChange` and `lfcSE` taken from the corresponding columns of the output table given by `DESeq2::results()`. However, when ...
deseq2 written 8 weeks ago by Homer0
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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 8 months 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 8 months ago by Homer0 • updated 8 months ago by Michael Love25k
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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 11 months ago by Homer0 • updated 11 months ago by Michael Love25k

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