Bioconductor Dependencies

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versions BiocVersion dependencies

updated 2.7 years ago by shepherl 3.6k • written 2.7 years ago by sohitmiglani • 0

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810

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R package dependencies

updated 4.7 years ago by Aaron Lun ★ 28k • written 4.7 years ago by MAPK • 0

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928

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cran package development dependencies

updated 5.1 years ago by Peter Langfelder ★ 2.8k • written 5.1 years ago by bjgrant • 0

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793

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dependencies error

updated 6.0 years ago by Aaron Lun ★ 28k • written 6.0 years ago by ericaugustoito • 0

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1.2k

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package installation dependencies bagfootr bagfoot

updated 6.1 years ago by Sean Davis 21k • written 6.1 years ago by rbronste ▴ 60

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2.1k

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scde ubuntu dependencies R

updated 6.8 years ago by Martin Morgan 25k • written 6.8 years ago by aditya531996 • 0

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deseq2 ubuntu edger dependencies

6.8 years ago aditya531996 • 0

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rhdf5 hdf5 dependencies

updated 7.4 years ago by Mike Smith ★ 6.2k • written 7.4 years ago by thabermann • 0

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parathyroidse package installation dependencies

updated 7.5 years ago by Hervé Pagès 16k • written 7.5 years ago by mmalek • 0

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2.5k

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annotationhub dependencies

8.0 years ago dalloliogm ▴ 50

10 results • Page 1 of 1

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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