Bioconductor Nested

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edgeR nested glm glmQLFit

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by jcalis ▴ 10

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edger nested estimatedispersions

9.2 years ago Mauve • 0

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deseq2 Phyloseq Nested

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by mpuli011 • 0

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nested DESeq2

updated 2.2 years ago by Michael Love 41k • written 2.4 years ago by yampolsk • 0

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deseq2 nested de

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by gaio.transposon • 0

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767

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deseq2 Paired Nested

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by julia.chariker ▴ 10

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edger nested design matrix differential expression

updated 9.2 years ago by Aaron Lun ★ 28k • written 9.2 years ago by Mauve • 0

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419

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DESeq2 multifactorial nested

updated 13 months ago by Basti ▴ 780 • written 13 months ago by jd • 0

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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…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

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Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

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Scholar to Rory Stark ★ 5.2k

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