Bioconductor RUVSeq

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336

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 6 days ago by James W. MacDonald 65k • written 6 days ago by Alexandre • 0

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261

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RUVSeq sva

20 days ago nhaus ▴ 30

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287

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RUVSeq limma DifferentialExpression

12 weeks ago • updated 11 weeks ago Shaimaa Gamal • 0

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347

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RUVSeq limma DifferentialExpression

updated 12 weeks ago by Gordon Smyth 50k • written 12 weeks ago by Shaimaa Gamal • 0

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362

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RUVSeq limma DifferentialExpression edgeR Normalization

updated 12 weeks ago by James W. MacDonald 65k • written 12 weeks ago by Shaimaa Gamal • 0

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452

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RUVSeq

3 months ago ctlong • 0

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669

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RUVSeq

updated 5 months ago by Michael Love 41k • written 6 months ago by myrthevanbaardwijk • 0

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1.2k

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RUVSeq sva limma

updated 13 days ago by Gordon Smyth 50k • written 7 months ago by Jonathan ▴ 10

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839

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BatchEffect RUVSeq RNASeq DESeq2

updated 7 months ago by ATpoint ★ 4.1k • written 7 months ago by Shashank • 0

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625

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RUVSeq DESeq2

9 months ago anne.hoffrichter • 0

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7.3k

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RUVg ruvseq rnaseq

updated 5 weeks ago by Shaimaa Gamal • 0 • written 9.0 years ago by Pauly Lin ▴ 150

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1.8k

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ruvseq

written 8.4 years ago by tonja.r ▴ 80

12 results • Page 1 of 1

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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…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Votes

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

C: Extremely big genes in annotation TxDb packages

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Scholar to Rory Stark ★ 5.2k

Popular Question to tangming2005 ▴ 190