Bioconductor Sweave

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Sweave rstudio

updated 9.6 years ago by Dan Tenenbaum ★ 8.2k • written 9.6 years ago by a.afshinfard ▴ 10

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Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…

Comment: athPkgBuilder data source :missing probesets by bobihanigujjar • 0

In this article, we'll explore the demand for unbranded BJJ Gis and the benefits of choosing unbranded Gis for customization. [does anyone …

Comment: Crossover design with limma by SamGG ▴ 360

IMHO, here are the missing annotations treatmentdrug_orderDrugPlac - treatmentplacebo_orderDrugPlac, # effect of drug for the Drug…

Answer: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k

You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…

Comment: makeContrastsDream for Interaction by abadgerw • 0

Thank you! I will try this out.

Votes

Comment: ANOVA like approach of edgeR

Comment: Crossover design with limma

Answer: DESeq2 normalization vs VST vs rlog

Comment: makeContrastsDream for Interaction

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