main effect estimation

Description

for rlmmain the main effects are estimated using rlm function from MASS package, with lmmain the OLS is used.

Usage

rlmmain(df,per=NULL)
lmmain(df,per=NULL)

Arguments

Value

lm,rlm

Author(s)

Elin Axelsson

See Also

rlm,lm

Examples

data(screen1_raw)
df = cellHTS2df(screen1_raw,neutral="Fluc")
df = weightDf(df,exclude=c("controlP1","controlP2","controlN1","controlN2","controlP1N1","double"))
mains = rlmmain(df)
hist(coef(mains))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(coRNAi)
Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/coRNAi/rlmmain.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LS main
> ### Title: main effect estimation
> ### Aliases: rlmmain lmmain
> 
> ### ** Examples
> 
> data(screen1_raw)
> df = cellHTS2df(screen1_raw,neutral="Fluc")
> df = weightDf(df,exclude=c("controlP1","controlP2","controlN1","controlN2","controlP1N1","double"))
> mains = rlmmain(df)
> hist(coef(mains))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>