Bioconductor Sizefactors

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4.9k

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normalization deseq2 sizefactors

updated 5.7 years ago by Michael Love 43k • written 5.7 years ago by mankadeep2 ▴ 40

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3.1k

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deseq2 Tximport Sizefactors normalizationfactors spike-in

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by Hina Bandukwala • 0

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3.4k

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deseq2 betaPrior=FALSE sizeFactors

updated 10.5 years ago by Michael Love 43k • written 10.5 years ago by elenigeorgopoulou86 ▴ 10

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2.8k

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edger estimatedisp scran sizefactors

updated 9.5 years ago by Aaron Lun ★ 29k • written 9.5 years ago by mnaymik ▴ 10

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1.6k

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deseq2 normalization sizefactors

updated 7.9 years ago by Michael Love 43k • written 8.0 years ago by René ▴ 40

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2.0k

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deseq2 sizeFactors

updated 8.2 years ago by Michael Love 43k • written 9.8 years ago by katzman ▴ 10

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2.2k

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scrnaseq scrn sizefactors

8.4 years ago sfpacman • 0

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2.2k

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deseq2 sizefactors pca normalization library size factor

updated 7.4 years ago by Michael Love 43k • written 7.4 years ago by ipso • 0

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3.6k

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tximport DESeq2 normalizationfactors sizefactors

updated 4.9 years ago by Michael Love 43k • written 4.9 years ago by svenbioinf • 0

9 results • Page 1 of 1

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Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k

There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…

Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0

@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…

Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0

Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …

Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k

Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …

Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20

You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…

Votes

Answer: Clarification on counting in Rsubread (featureCounts)

Comment: Clarification on counting in Rsubread (featureCounts)

C: ControlGenes/ housekeeping genes Deseq2

Answer: Clarification on counting in Rsubread (featureCounts)

C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results

Awards • All

Commentator to James W. MacDonald 68k

Great Question to fl ▴ 20

Popular Question to Lluís Revilla Sancho ▴ 760