Bioconductor S4

Showing : s4 • reset

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715

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DBI S4 Biobase

updated 15 months ago by Hervé Pagès 16k • written 16 months ago by sandmann.t ▴ 70

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707

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S4 Rcpp InteractionSet IRanges Rle

updated 3.5 years ago by Aaron Lun ★ 28k • written 3.5 years ago by lklei001 • 0

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673

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calcium imaging imaging s4

updated 3.7 years ago by shepherl 3.6k • written 3.7 years ago by muad.abdelhay ▴ 10

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555

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class S4

updated 3.8 years ago by Hervé Pagès 16k • written 3.8 years ago by Teun van den Brand • 0

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863

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s4 dataframe left_join merge

updated 4.6 years ago by Hervé Pagès 16k • written 4.6 years ago by Michael Steinbaugh ▴ 90

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873

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s4 generic

updated 4.8 years ago by Marcel Ramos 680 • written 4.8 years ago by Michael Steinbaugh ▴ 90

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649

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S4 deseq2

updated 4.9 years ago by swbarnes2 ★ 1.3k • written 4.9 years ago by shintzen • 0

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863

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s4 methods SummarizedExperiment

updated 4.9 years ago by Aaron Lun ★ 28k • written 4.9 years ago by brendan.innes ▴ 10

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937

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devtools S4 methods cache

5.0 years ago Michael Steinbaugh ▴ 90

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868

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S4 packages

updated 5.3 years ago by Michael Lawrence 11k • written 5.3 years ago by lukaszbednarz ▴ 10

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998

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iranges integerlist s4

7.3 years ago Jurat Shahidin ▴ 80

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1.1k

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s4 coercion iranges integerlist

7.3 years ago jian_liangli • 0

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mclust s4vectors S4 as.matrix .FCS

7.5 years ago anara92 • 0

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10k

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genomicranges grangeslist granges s4

updated 20 months ago by Hervé Pagès 16k • written 7.5 years ago by richierocks ▴ 40

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1.6k

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rnbeads error as.vector(data) s4vectors s4

8.3 years ago schasse • 0

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4.8k

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updated 8.7 years ago by Michael Lawrence 11k • written 8.7 years ago by Koen Van den Berge ▴ 180

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2.5k

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lumi S4

8.8 years ago Chi Hong • 0

17 results • Page 1 of 1

Recent ...

Replies

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