GEO_AddDesignList: AddDesignList

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

After getElist and make a DesignList.

Usage

  AddDesignList(eset,
              factor,
              levels,
              control.probes,
              array.annotation,
              NA.method = c("one","all")[1],
              normalizeBetweenArrays=F)

Arguments

factor	a group defined vector.
levels	the levels of factor.Note that Control should be placed last.
control.probes	a list of control probe information including control.col and control.symbol
array.annotation	array annotation information including probeid.col,symbol.cols,anno.cols,sequence.col and db.anno.
NA.method	one of "one" and "all".one means the row should be deleted just as one NA value exists,and all means the row should be deleted only when all elements were NA value.Default is "one".

Value

DesignList Object

Author(s)

Weibin Huang

Examples

## parameters
factor = ifelse(pdata$pnstage == "N0","N0","Np")
levels = c("Np","N0") # factor的level
control.probes = list(
   l1=list(control.col="Probe_Type",control.symbol = c("A","I")),
   l1=list(control.col="Source",control.symbol = "ILMN_Controls"))
array.annotation = list(
     probeid.col="ID",
     symbol.cols=c("Symbol","Unigene_ID","Entrez_Gene_ID"),
     anno.cols=c("SYMBOL","UNIGENE","ENTREZID"),
     sequence.col = "SEQUENCE",
     db.anno=common.annot)
## Running
AddDesignList(eset,
              factor,
              levels,
              control.probes,
              array.annotation,
              NA.method = c("one","all")[1],
              normalizeBetweenArrays=F)

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.