## User: Homer

Homer •

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- 11 months, 1 week ago
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#### Posts by Homer

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... 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
Homer •

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... 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 ...

written 6 weeks ago by
Homer •

**0**• updated 6 weeks ago by Gordon Smyth ♦**39k**2

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... 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 ...

written 7 weeks ago by
Homer •

**0**• updated 7 weeks ago by Gordon Smyth ♦**39k**0

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... Thanks a lot for your answer. I'll try to conduct a power/error analysis based on simulated data. ...

written 8 weeks ago by
Homer •

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... 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 ...

written 8 weeks ago by
Homer •

**0**• updated 8 weeks ago by Michael Love ♦**25k**0

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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
Homer •

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... 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 ...

written 8 weeks ago by
Homer •

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... 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
Homer •

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... 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 ...

written 8 months ago by
Homer •

**0**• updated 8 months ago by Michael Love ♦**25k**1

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... 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 ...

written 11 months ago by
Homer •

**0**• updated 11 months ago by Michael Love ♦**25k**#### Latest awards to Homer

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