DiffAnalysis.unpaired {anapuce} R Documentation

## Differential Analysis for unpaired data

### Description

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

### Usage

DiffAnalysis.unpaired(fileIN = "resNorm.txt", n = 3, cond1 = "cond1.",
cond2 = "cond2.", fileOUT = "ListOfGenes.txt",
fileDelete = "GenesOutOfAnalysis.txt", procs = c("bonferroni", "BH"),
alpha = c(0.05, 0.05), 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. cond1  a regular expression corresponding to the first condition. cond2  a regular expression corresponding to the second condition. 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 fileDelete  output data file containing the list of withdrawn genes.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. 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 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- The list of withdrawn genes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.

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

p.adjust, MeanBySpot, DiffAnalysis
data(apo)