rowaov: Gene by gene ANOVA function

In LMGene: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

Description

Computes the mean squares and degrees of freedom for gene-by-gene ANOVAs.

Usage

rowaov(eS, model=NULL)

Arguments

eS	An ExpressionSet object. Any transformation and normalization of eS should be done prior to use in rowaov.
model	Model used for comparison. See details and LMGene.

Details

If you have data in a matrix and information about experimental design factors, then you can use neweS to convert the data into an ExpressionSet object. Please see neweS for more detail.

The model argument is an optional character string, constructed like the right-hand side of a formula for lm. It specifies which of the variables in the ExpressionSet will be used in the model and whether interaction terms will be included. If model=NULL, it uses all variables from the ExpressionSet without interactions. Be careful of using interaction terms with factors; this often leads to overfitting, which will yield an error.

Value

resmat

A matrix of MSEs and degrees of freedom for all model factors and all genes. The first rows of resmat contain MSE's for each effect in model, ending with the residual MSE. The remaining rows contain degrees of freedom for each effect in the model, ending with the residual d.f. Each column corresponds to a gene.

Author(s)

David Rocke and Geun-Cheol Lee

References

David M. Rocke (2004), Design and analysis of experiments with high throughput biological assay data, Seminars in Cell & Developmental Biology, 15, 703–713.

http://dmrocke.ucdavis.edu

See Also

genediff, LMGene

Examples

library(Biobase)
library(LMGene)

#data
data(sample.mat)
data(vlist)

raw.eS <- neweS(sample.mat, vlist)

# glog transform data
trans.eS <- transeS(raw.eS, lambda = 727, alpha = 56)

# Perform gene-by-gene anova
resmat <- rowaov(trans.eS)
resmat[,1:3]

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Loading required package: multtest
Loading required package: survival
Loading required package: affy

Attaching package: 'LMGene'

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

    norm

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
           [,1]       [,2]        [,3]
[1,]  0.4868864  0.2906989  0.14301286
[2,]  0.5660385  0.4771193  0.27677382
[3,]  0.1084851  0.1354793  0.08015563
[4,]  7.0000000  7.0000000  7.00000000
[5,]  1.0000000  1.0000000  1.00000000
[6,] 23.0000000 23.0000000 23.00000000

LMGene documentation built on April 28, 2020, 8:01 p.m.