User: Smith, Hilary A

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Posts by Smith, Hilary A

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Answer: A: edgeR - R script - results compared to DESeq
... In case it helps the discussion ... I also tried running GLMs in both DESeq and edgeR. I likewise found that edgeR yielded more differentially expressed tags or genes. I know Dr. Gordon Smyth mentioned calcNormFactors and tagwise dispersion; I did use both of these options. If it helps, an abstract ...
written 7.9 years ago by Smith, Hilary A40
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Answer: A: TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq
... Thank you very much, and thank you for posting the code to allow baySeq to use the calcNormFactors/TMM normalization. Best, Hilary ----- Original Message ----- From: "Gordon K Smyth" To: "Hilary A Smith" Cc: "Bioconductor mailing list" , "Thomas J Hardcastle" Sent: Friday, November 18, 2011 10:1 ...
written 7.9 years ago by Smith, Hilary A40
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Answer: A: baySeq plotPosteriors or plotMA question
... Hello, I'm working on a couple analyses (currently pairwise) for 3'-DGE. Using baySeq, edgeR, and DESeq are yielding different answers; specifically DESeq and baySeq find different subsets of the genes found by edgeR. In trying to isolate the discrepancy, I've been trying to make items like normaliz ...
written 7.9 years ago by Smith, Hilary A40
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baySeq plotPosteriors or plotMA question
... Hello, I'm a graduate student and just starting to analyze my first set of RNA-Seq data (so learning R/Bioconductor). In using the baySeq program, I am slightly confused about how to color-code the significant values in the plotPosteriors (and plotMA) functions. The vignette includes the example be ...
written 8.0 years ago by Smith, Hilary A40

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