tileplot.double: TilePlot 2-array Microarray Processing Function

In TilePlot: Characterization of functional genes in complex microbial communities using tiling DNA microarrays

Description

This function is for processing a two functional gene tiling DNA microarrays of the same design for the purposes of comparison. As input it takes array data, and its output is the hybridization plot for each gene on the array, the mean probe intensity, the median probe intensity, the bright probe fraction, the bright segment length dependent score, the mean bright probe intensity, and the median bright probe intensity. The data for array2data can be normalized to the array1data using loess - ie an assumption is made that all spots on both arrays should be approximately the same, then all array2data is adjusted to fit that assumption - the modified array2data is given as output in the graphdirectory. The output is both graphical (as a set of tex and encapsulated-postscript format files that can be assembled using latex) and a tab-delimited text file with rows corresponding to genes and columns corresponding to output parameters.

Usage

tileplot.double(genesonchip, array1data, array2data, annotationslist, cutoff,
cutoff_multiplier = 3, outputfile, graphdirectory, outputtable, array1name = "Array 1",
array2name = "Array 2", loess = TRUE, smoothing_factor = 6)

Arguments

genesonchip	Path to a text file containing a list of all gene identifiers (I try to use IMG/M identifiers) on the microarray.
array1data	Path to a tab-delimited text file for the first array containing all probe identifiers in the first (left-hand) column and probe intensities in the second (right-hand) column. File must be ordered in a specific way (see below).
array2data	Path to a tab-delimited text file for the second array containing all probe identifiers in the first (left-hand) column and probe intensities in the second (right-hand) column. File must be ordered in a specific way (see below).
annotationslist	Path to a text file containing a list of all gene annotations. Each annotation must contain the gene identifier mentioned in genesonchip
cutoff	An integer cutoff value for distinguishing dark probes from bright probes based on probe intensity value. This is optional - the default value is three times the median value for all probes on Array 1.
cutoff_multiplier	Alternatively the cutoff can be expressed as a multiple of the median value for all probes on the array. The default is 3, but in case you wish to trade off specificity for sensitivity (or vice versa) in complex samples then you can set the multiplier lower (or higher) using this parameter.
outputfile	Path leading to desired output filename (a .tex file for input into latex).
graphdirectory	A directory for output of plots in encapsulated postscript format.
outputtable	Path leading to desired output filename (a .tdt file for further analysis of statistics for each individual gene).
array1name	Identifier for Array 1 (Default is "Array 1").
array2name	Identifier for Array 2 (Default is "Array 2").
loess	Use loess normalization? TRUE or FALSE. TRUE is the default.
smoothing_factor	Smoothing factor for BPF recommendation. The default of 6 is usually OK.

Details

All probe names must have the following format: geneidentifier-probenumber. array1data must be sorted so that the probes for each gene are in the correct order (ie from probe 1 to the final probe). This is easily achieved with the unix sort command (sort -n -k2 -t- filename > sorted\_filename). The output file should be processed with LaTeX (http://www.latex-project.org/) to obtain a PDF.

Author(s)

Ian Marshall

References

http://www.stanford.edu/~ianpgm/tileplot

Examples

#This example code will deposit tex, tdt, and eps output into your R session directory
tileplot.double(genesonchip=system.file("allgenesonchip.ID", package="TilePlot"),
array1data=system.file("array1", package="TilePlot"),
array2data=system.file("array2", package="TilePlot"),
annotationslist=system.file("all_annotations", package="TilePlot"),
outputfile=file.path(tempdir(), "example_output.tex"),  graphdirectory=tempdir(),
outputtable=file.path(tempdir(), "example_output.tdt"))

TilePlot documentation built on May 30, 2017, 6:56 a.m.