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Gordon Smyth
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Comment: Differences in differential analysis methods for RNA-Seq
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ATpoint
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> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level
edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
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Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
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ATpoint
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There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
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MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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Yveto
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Thank for your response. It is Illumina 450 K. I use this code
```{r }
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annotat…
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