SD Assessment Functions

Description

These functions create assessments, figures, and tables for expression standard errors

Usage

affycomp.figure7(l,main="Figure 7")
affycomp.compfig7(l,method.names=as.character(1:length(l)),
                  main="Figure 7")
tableSD(l,method.names=NULL)

Arguments

Details

This uses the dilution data. The exprsets need to have standard error estimates in the assayDataElement(exprset,"se.exprs"). Read the vignette for more details. The functions work similarly to those assessing expression measures.

All these files need the result of assessSD

Value

Depends on the call.

Author(s)

Rafael A. Irizarry

Examples

library(affycompData)
data(rma.sd.assessment) ##this was produced with affycomp.assess
data(lw.sd.assessment) ##this one too
affycomp.compfig7(list(rma.sd.assessment,lw.sd.assessment))
affycomp.figure7(rma.sd.assessment)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(affycomp)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affycomp/SD.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SD
> ### Title: SD Assessment Functions
> ### Aliases: SD tableSD affycomp.figure7 affycomp.compfig7
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(affycompData)
> data(rma.sd.assessment) ##this was produced with affycomp.assess
> data(lw.sd.assessment) ##this one too
> affycomp.compfig7(list(rma.sd.assessment,lw.sd.assessment))
> affycomp.figure7(rma.sd.assessment)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>