do_DEG_2groups: Do differential expression analysis for the expression matrix

In jmzeng1314/humanid: gene id annotation

Description

please make sure that there are just two group for you expression matrix, you should modify the code in this function if there's more than 2 group. I highly suggest you to use Limma to analysis,it's very easy, but you should make sure that relevel(factor(group_list),'control')

Usage

do_DEG_2groups(prefix = "GSE1009", exprSet = example_exprSet, group_list,
  method, destdir = ".")

Arguments

prefix	The prefix for all of the output files.( we don't need it now actually)
exprSet	Matrix with microarray expression values.
group_list	Factors for two groups that are tested for differential expression.please make sure that relevel(factor(group_list),'control')
method	which method do you choose, limma,samr,rowttest in genefilter,resamplingPvalues in BioNet,t.test
destdir	where to store the files just download.( we don't need it now actually)

Value

a data.frame just like topTable

Examples

#' do_DEG_2groups('CLL',exprSet,group_list,method='limma')

jmzeng1314/humanid documentation built on May 19, 2019, 2:57 p.m.