Bioconductor Glmfit

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edger edger main and interaction effects glmfit

updated 6.5 years ago by Aaron Lun ★ 28k • written 6.5 years ago by D ▴ 10

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edger rnaseq glm glmfit

updated 8.4 years ago by Aaron Lun ★ 28k • written 8.4 years ago by alessia.donato • 0

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edger standard error glmfit

8.4 years ago david.hughes • 0

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edger glmfit glmlrt()

updated 9.1 years ago by Aaron Lun ★ 28k • written 9.1 years ago by cadeans • 0

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Comment: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k

The poster needs to run Salmon with `--numGibbsSamples=50`. I suspect that nf-core just won't do that, so Salmon needs to be run directly.

Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k

Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.

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…

Votes

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

Comment: ANOVA like approach of edgeR

Comment: Crossover design with limma

Answer: DESeq2 normalization vs VST vs rlog

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