Bioconductor Volcano plot

Showing : volcano plot • reset

vote

961

views

DiffBind volcano plot software error

6.3 years ago rbronste ▴ 60

votes

replies

1.6k

views

volcano plot rna seq

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by adeler001 • 0

votes

replies

2.0k

views

Volcano plot Parameters

updated 8.4 years ago by Gordon Smyth 53k • written 8.4 years ago by Sanches • 0

votes

1.7k

views

limma volcano plot

updated 8.8 years ago by Gordon Smyth 53k • written 8.8 years ago by yul • 0

votes

replies

2.7k

views

volcano plot edgr

9.0 years ago elena.capel ▴ 10

votes

replies

1.6k

views

microarray limma volcano plot

updated 11.3 years ago by Gordon Smyth 53k • written 11.3 years ago by jyoti_cad • 0

6 results • Page 1 of 1

Recent ...

Replies

Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0

Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k

I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0

Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…

Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0

Hello, I was also wondering about the same issue. Did you figure it out?

Votes

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

Awards • All

Scholar to Gordon Smyth 53k

Popular Question to Peter Hickey ▴ 760