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deseq2 extracting contrasts rnaseq interaction term

updated 5.8 years ago by swbarnes2 ★ 1.3k • written 5.8 years ago by Amit Indap ▴ 10

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deseq2 multiple factor design nested design interaction term

updated 7.0 years ago by Michael Love 41k • written 7.0 years ago by zahra.aboukhalil • 0

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deseq2 interaction term

updated 6.6 years ago by Michael Love 41k • written 6.7 years ago by sofiagreen72211 ▴ 10

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deseq2 sva interaction term grouping variable deseq

6.3 years ago kevin.kingsland ▴ 70

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deseq2 ANOVA design interaction term

updated 6.2 years ago by Michael Love 41k • written 6.2 years ago by tarun2 • 0

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deseq2 design interaction term R

6.2 years ago briverog • 0

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deseq2 multiple factor design interaction term

updated 6.2 years ago by Michael Love 41k • written 6.2 years ago by Giovanni Bacci • 0

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deseq2 interaction term multiple groups betaprior

updated 6.0 years ago by Michael Love 41k • written 6.0 years ago by tarun2 • 0

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deseq2 lfcshrink interaction term

updated 6.0 years ago by Michael Love 41k • written 6.0 years ago by krutherford • 0

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deseq2 interaction term

updated 5.6 years ago by Michael Love 41k • written 5.6 years ago by Cece • 0

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deseq2 interaction term

5.6 years ago guipagui • 0

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deseq2 deseq limma interaction term

updated 7.0 years ago by Simon Anders ★ 3.7k • written 7.0 years ago by sbcn ▴ 80

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deseq2 multifactor interaction term gender effect 3-factors

updated 5.0 years ago by Michael Love 41k • written 5.0 years ago by kmu004 ▴ 50

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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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A: Error in DESeqDataSet : some values in assay are not integers

Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

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