Package TilePlot. April 8, 2011

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1 Type Package Package TilePlot April 8, 2011 Title This package analyzes functional gene tiling DNA microarrays for studying complex microbial communities. Version 1.1 Date Author Ian Marshall Maintainer Ian Marshall This package is intended for processing the output from functional gene tiling DNA microarray experiments. It produces hybridization pattern plots for each gene on the array, and statistics for each gene including mean probe intensity, median probe intensity, bright probe fraction, bright segment length dependent score, bright probe mean intensity, and bright probe median intensity. Output is generated in order of bright segment length dependent score in both a latex/eps format and tab-delimited text file. The package works in three modes: single array, comparison of two arrays, and comparison of two arrays with loess normalization. License GPL-2 LazyLoad yes Repository CRAN Date/Publication :11:52 R topics documented: TilePlot-package compareplot tileplot.multi tileplot.multi.loess tileplot.single Index 8 1

2 2 compareplot TilePlot-package Package for analysis of Functional Gene Tiling DNA Microarray Details This package is intended for processing the output from functional gene tiling DNA microarray experiments. It produces hybridization pattern plots for each gene on the array, and statistics for each gene including mean probe intensity, median probe intensity, bright probe fraction, bright segment length dependent score, bright probe mean intensity, and bright probe median intensity. Output is generated in order of bright segment length dependent score in both a latex/eps format and tab-delimited text file. The package works in three modes: single array, comparison of two arrays, and comparison of two arrays with loess normalization. Package: TilePlot Type: Package Version: 1.0 Date: License: GPL-2 LazyLoad: yes Ian Marshall <ianpgm@stanford.edu> compareplot Function for comparing two vectors and performing linear regression Usage This function is used internally by tileplot.multi and tileplot.multi.loess to produce scatterplots with linear regression for all probes on the microarray or other whole-microarray vectors of parameters like gene median probe intensity etc. compareplot(arrayset1, arrayset2, array1label, array2label, title)

3 tileplot.multi 3 Arguments arrayset1 The first vector of microarry data arrayset2 The second vector of micrarray data array1label The identifying label for array 1 array2label The identifying label for array 2 title The title to be printed for the plot Ian Marshall tileplot.multi TilePlot 2-array Microarray Processing Function Usage 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 output is both graphical (as a set of tex and encapsulatedpostscript 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. tileplot.multi(genesonchip, array1data, array2data, annotationslist, cutoff, output Arguments genesonchip array1data Path to a text file containing a list of all gene identifiers (I try to use IMG/M identifiers) on the microarray. 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 (righthand) 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

4 4 tileplot.multi.loess Details cutoff An integer cutoff value for distinguishing dark probes from bright probes based on probe intensity value. 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"). 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. Ian Marshall Examples #This example code will deposit tex, tdt, and eps output into your R session directory tileplot.multi(genesonchip=system.file("allgenesonchip.id", package="tileplot"), array1data tileplot.multi.loess TilePlot 2-array Microarray Processing Function with loess normalization 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 is 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.

5 tileplot.multi.loess 5 Usage tileplot.multi.loess(genesonchip, array1data, array2data, annotationslist, cutoff, Arguments genesonchip array1data Path to a text file containing a list of all gene identifiers (I try to use IMG/M identifiers) on the microarray. 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 (righthand) 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. 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"). 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. Ian Marshall Examples #This example code will deposit tex, tdt, and eps output into your R session directory tileplot.multi.loess(genesonchip=system.file("allgenesonchip.id", package="tileplot"), arra

6 6 tileplot.single tileplot.single TilePlot Single Microarray Processing Function Usage This function is for processing a single functional gene tiling DNA microarray. 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 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. tileplot.single(genesonchip, array1data, annotationslist, cutoff, outputfile, graph Arguments Details 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 containing all probe identifiers in the first (lefthand) 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. 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"). 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. Ian Marshall

7 tileplot.single 7 Examples #This example code will deposit tex, tdt, and eps output into your R session directory tileplot.single(genesonchip=system.file("allgenesonchip.id", package="tileplot"), array1dat

8 Index compareplot, 2 TilePlot (TilePlot-package), 2 tileplot (TilePlot-package), 2 TilePlot-package, 2 tileplot.multi, 3 tileplot.multi.loess, 4 tileplot.single, 6 8