User: AS

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AS0
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Posts by AS

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Comment: C: Differential gene expression of time series RNAseq expermimnet with one cohort (
... Sorry for the late reply--got side tracked. I'm basing this answer off of what I know about general linear model regression testing which should still be applicable--I think. I'm going to explain some regression stuff below for the sake of clarity--forgive me if you already understand this. When y ...
written 11 weeks ago by AS0
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Comment: C: limma voom Mean-variance trend plot: x-axis?
... Sorry for the offense--it was completely unintentional. I've just started to work in this sphere so I'm still trying to get a handle on code, math, and statistics. Given the sqrt(sigma) y-axis label on the plotSA graph, I just wasn't sure if it was just a different way expressing the same thing. Tha ...
written 11 weeks ago by AS0
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Comment: C: limma voom Mean-variance trend plot: x-axis?
... Thanks. This plot was saved prior to the loess line. ...
written 11 weeks ago by AS0
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Comment: C: Differential gene expression of time series RNAseq expermimnet with one cohort (
... Back up a little bit, how did you create your original dds variable--the DESeq object? What was the design you had for that? You would have used some function like DESeqDataSetFromMatrix() or something similar to it. With the code you've posted, the only difference is whether or not you're doing a ...
written 11 weeks ago by AS0
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limma voom Mean-variance trend plot: x-axis?
... Hi all, I've been following the "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR" vignette for usign limma on miRNA-seq data. I've gotten to the point of comparing the mean-variances pre- and post-filtering my data based on CPM counts. I'm a bit bugged by the differences in x-axis l ...
limma written 11 weeks ago by AS0

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