DiffAnalysis {anapuce}

Differential Analysis for paired data

Description

Performs the differential analysis from normalised paired microarray data according to different ways of variance modelling and computes lists of differentially expressed genes according different multiple testing procedures.

Usage

DiffAnalysis(fileIN = "resNorm.txt", n = 3, ind.array = 1:2, name.A = "A",
name.M = "M.norm", fileOUT = "ListOfGenes.txt",
fileDelete = "GenesOutOfAnalysis.txt", procs = c("bonferroni", "BH"),
alpha = c(0.05, 0.05), dyeswap = TRUE, indDS = c(2), fileID = NULL,
function.trt = NULL, by.var = "ID", varmixt.meth = TRUE, header = TRUE,
sep = "\t", sep.write = "\t", dec.write = ".", ...)

Arguments

fileIN

normalized data set.

n

number of identificant columns.

ind.array

the indices of arrays to analyze.

name.A

character string containing a regular expression contained in the columnames corresponding to the A values.

name.M

character string containing a regular expression contained in the columnames corresponding to the M values.

fileOUT

output data file.

fileDelete

output data file containing the list of withdrawn genes.

procs

adjusting p-values procedures to be used.

alpha

values of the first type error to be used in the different procedures.

dyeswap

logical indicating whether the design is a dye swap.

indDS

index of arrays related to dye swap.

fileID

file giving information about genes.

function.trt

function to be applied before differential analysis.

by.var

argument passed to function.trt.

varmixt.meth

logical indicating whether to perform the variance modelling proposed by Delmar et al. (2005).

header

a logical value indicating whether the file contains the names of the variables as its first line. Used in the read.table function.

sep

the field separator string to use in the read.table function.

sep.write

the field separator string to use in the write.table function.

dec.write

the string to use for decimal points in the write.table function.

...

Further arguments to be passed to read.table.

Details

This function performs a differential analysis in the gene-specific and homoscedastic cases. If varmixt.meth = TRUE, the method used is the method proposed by Delmar et al. (2005), (the same as coded in the vm.analysis.paired function from the varmixt package.)

Value

By default these following files are created

- one list of differentially expressed genes by procedure

- The list of withdrawn genes

- The list of all the genes

An R object is returned if function return value is assigned.

Author(s)

J. Aubert

References

Delmar, P., Robin, S. and Daudin, J.J., (2005), VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data, Bioinformatics, 21,(4), 502–8

Dudoit, S., Yang, Y. H., Callow, M. J. and Speed, T.P., (2002), Statistical methods for identifying differentially expressed genes in replicated cdna microarray experiments, Statisticia Sinica, 12, 111–139

See Also

p.adjust, MeanBySpot, DiffAnalysis.unpaired

Examples

data(spleen)
# Analysis on the first 100 genes
resSpleen <- DiffAnalysis(spleen[1:100, ], n = 1, ind.array = 1:6, name.A = "A.", name.M = "M.",
varmixt.meth = TRUE, dyeswap = TRUE, indDS = c(2,4,6))
# Histogramm of the raw-pvalues
# hist(resSpleen$PValueVM)