affycoretools (version 1.38.0)

foldFilt: Output Fold Change Data

Description

This function is designed to take an ExpressionSet and some comparisons and output either HTML tables, text files, or both.

Usage

foldFilt(object, fold = 1, groups, comps, compnames, save = FALSE, text = TRUE, html = TRUE, filterfun = NULL)

Arguments

object

An ExpressionSet object

fold

The log fold change cutoff to use. Note that this is log base two.

groups

A vector of group identifiers. Probably easiest to use a numeric vector

comps

A list containing all the comparisons to be made. Each list item should be a vector of length two. See details for more information.

compnames

A character vector of the names for each of the comparisons to be made. This will be the name of the resulting HTML or text file.

save

Boolean. If TRUE, a list will be returned. The first item in the list will be a vector showing the number of 'significant' genes for each comparison. The second item will be a matrix of -1's, 0's and 1's indicating a significant difference, and the direction of the difference. The first item is useful for creating Sweave - based reports and the second is useful for making Vennn diagrams using the vennDiagram from the limma package.

html

Boolean - if TRUE, output HTML tables

text

Boolean - if TRUE, output text tables

filterfun

A filtering function, created by genefilter to filter the data using additional criteria. See details for more information

Value

Returns a list; see above for the elements of the list. This function is mainly called for the side effect of outputting HTML or text files containing annotated 'significant' gene lists.

Details

This function is useful for outputting annotated gene lists for multiple fold change comparisons. The genes will be ordered by the absolute fold change. Note that this function is essentially a wrapper to call annaffy, so is only useful for Affymetrix GeneChips for which there is an annotation package.

Without attaching a data file to this package, it is not possible to give a working example. Instead, here is a 'for instance'.

Say you have an ExpressionSet containing four Affy HG-U133Plus2 chips. There is no replication, and you simply want to output genes with a two-fold or greater difference between the first chip and each of the last three (the first chip is the control, and the other three are experimentals). The ExpressionSet is called eset.

Additionally, say we don't want any genes called significant if both of the samples have very low expression. We can set up a filter using the genefilter package.

f1 <- kOverA(1,6)

filt <- filterfun(f1)

foldFilt(eset, groups=1:4, comps=list(c(2, 1), c(3, 1), c(4, 1)), compnames=c("Expt1-Cont","Expt2-Cont","Expt3-Cont"), filterfun = filt)

This will output three HTML tables called 'Expt1-Cont.html', etc., each containing sorted genes that have two-fold or greater differences between the two samples.