Bioconductor Paired-end reads

Showing : paired-end reads • reset

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974

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diffbind paired-end reads

updated 3.1 years ago by Rory Stark ★ 5.1k • written 6.9 years ago by rbronste ▴ 60

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1.3k

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paired-end reads bam file

6.1 years ago ioannis.vardaxis ▴ 30

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1.1k

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dnaseq rtracklayer paired-end reads

6.4 years ago zwfanwz678 • 0

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1.1k

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summarizeoverlaps paired-end reads readGAlignmentPairs

6.7 years ago teresati ▴ 10

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836

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quasr quasr error paired-end reads rnaseq

6.9 years ago guillaume.dachy • 0

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953

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quasr paired-end reads rnaseq

6.9 years ago guillaume.dachy • 0

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868

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quasr rnaseq paired-end reads

7.0 years ago guillaume.dachy • 0

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1.4k

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rsamtools paired-end reads countbam

updated 7.2 years ago by Martin Morgan 25k • written 7.2 years ago by Dario Strbenac ★ 1.5k

8 results • Page 1 of 1

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Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0

I see. Do you recommend a certain method to get norm.factors through calcNormFactors function espcially if the downstream analysis includes…

Comment: Can the limma package be applied to Log2 RUV-normalized data? by Gordon Smyth 49k

515 samples is certainly large enough.

Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0

Thank you for your kind response Gordon! :) Have a good time at the end of the year! Best, Yujin Kim

Comment: Agilent Microarray Gene Oncology analysis gone wrong by SamGG ▴ 320

Gordon said to let coef to its default value: topTable(fit, n=20)

Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0

Hi Gordon, On what basis we can determine whether the dataset is large or not? I am working on a dataset of 515 samples and 5440 genes. I w…

Votes

Comment: Can the limma package be applied to Log2 RUV-normalized data?

Answer: Correct the batch effect in methylation analysis in R

Comment: Why is DMRcate not available for Bioconductor version 3.18?

Answer: Correct the batch effect in methylation analysis in R

Awards • All

Scholar to Gordon Smyth 49k

Popular Question to Lluís Revilla Sancho ▴ 720

Popular Question to Frederik Ziebell ▴ 20