GEO_AddDesignList: AddDesignList

Description Usage Arguments Value Author(s) Examples

Description

After getElist and make a DesignList.

Usage

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  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

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## parameters
factor = ifelse(pdata$pnstage == "N0","N0","Np")
levels = c("Np","N0") # factorçš„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.