Bioconductor Pcatools

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DESeq2 PCAtools

updated 5 days ago by Michael Love 41k • written 7 days ago by Aaliya • 0

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DESeq2 RSTUDIO PCAtools

updated 7 days ago by swbarnes2 ★ 1.3k • written 8 days ago by Aaliya • 0

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edgeR PCAtools

updated 4 weeks ago by Gordon Smyth 50k • written 4 weeks ago by Fabian • 0

3 results • Page 1 of 1

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Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k

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) by Yveto • 0

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 by Rory Stark ★ 5.2k

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) by Michael Love 41k

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) by HAK • 0

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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Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

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