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Comment: Differences in differential analysis methods for RNA-Seq
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ATpoint
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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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Thank for your response. It is Illumina 450 K. I use this code
```{r }
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
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I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
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But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed):
```
limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
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Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
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