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## Rawdata
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The Rawdata directory contains the original datafiles from the respective platforms
Illumina: output from BeadScan software with setting <SaveTextFiles>true</SaveTextFiles> in "Settings.xml" to obtain intensity values, and the GenCall software version 6.0.7 for genotypes.
Affymetrix: output copy number analysis from dChip v 1.3
BACarray: Genepix 4.1 .GPR files, and the corresponding .gal file

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## Processeddata
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The Processeddata directory contains textfiles with copynumber results from each method. The affymetrix, and BAC-file only contain data from the 4 fresh frozen tumor samples (44TV, 106TV, 108TV and 514TV). The illumina datafile also contains data from the praffin embedded tumor samples (44TP, 106TP, 108TP and 514TP) and leukocyte DNA (44NB, 106NB, 108NB and 514NB)
The first two columns of these files are the chomosome and the chomosomal position of the probes.


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## Analysis
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The analysis is performed using the R-package beadarraySNP which is available in the Analysis directory. This package has the following dependencies:
- quantsmooth (also in Analysis directory)
- Biobase (Bioconductor)
- limma (Bioconductor) 
- lodplot (CRAN)
- quantreg (CRAN)

The package was developed and tested using R 2.4.0 and Bioconductor 1.9

The scripts to create the figures and table from the paper "High Resolution Copy Number Analysis of Paraffin Embedded Archival Tissue Using SNP BeadArrays" are also in the Analysis directory. In order to load the correct datafiles it is important to set the working directory at the beginning of each script to the base directory of the archive (containing the directories: Analysis, ProcessedData and Rawdata)

Description of scripts:
createdatafiles.r  Using the Raw data, create the .RData files used for creating the figures, and save the processed data text files.
figure1.r  Create figure1.pdf (properties of the data)
figure2.r  Create Figure2.pdf (Comparison of normalization settings)
figure3.r  Create Figure3.pdf (comparison of methods)
figure4.r  Create Figure4.pdf (comparison of fresh frozen and FFPE tissue)
figure5.r  Create Figure5.pdf (Copy number and LOH analysis on a set of 22 tumors from FFPE material)
tables.r      Calculate the contents of the tables in the paper