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Appendix a Details on Selected Resources Appendix A Details on selected resources A.1 Data sets Here we describe three data sets that are used in many different examples throughout the book. A.1.1 ALL The ALL data were reported by Chiaretti et al. (2004) The data were normalized using quantile normalization, and expression estimates were computed using RMA (Irizarry et al., 2003b). We consider the comparison of the 37 samples from patients with the BCR/ABL fusion gene resulting from a chromosomal translocation (9;22) with the 42 samples from the NEG group. They are available in the R package ALL. A.1.2 Renal cell cancer The kidpack package contains gene expression data from 74 renal cell carci- noma (RCC) patient biopsy samples (Sultmann¨ et al., 2005). The samples were hybridized to two-color cDNA arrrays with PCR products of 4224 clones spotted in duplicate. These clones had been selected by their pre- sumed relevance to cancer and on the basis of a previous genome-wide array study of kidney cancer. A pool of various RCC samples was used as a reference sample, which was always labeled with the red dye. The data were normalized with the vsn package, and we base our analysis on the generalized log-ratio values quantifying the difference between the tumor samples and the reference sample. The exprSet object esetSpot contains the normalized expression values and patient data. The RCC samples belong to three different histological types, clear cell (ccRCC), papillary (pRCC), and chromophobe (chRCC). A.1.3 Estrogen receptor stimulation The data are from eight samples from an estrogen receptor positive breast cancer cell line. After serum starvation, four samples were exposed to es- trogen and then harvested for analysis with Affymetrix human genome U-95Av2 genechips after 10 hours for two samples and 48 hours for the other two. The remaining four samples were left untreated and harvested 444 AppendixA. Details onSelectedResources at corresponding times. The data are explained in more detail by Scholtens et al. (2004) and are available in the estrogen package. A.2 URLs for projects mentioned Below, we list URLs for different projects and computational resources that were discussed in the text. AmiGO http://www.godatabase.org/ BioCarta www.biocarta.com Bioconductor www.bioconductor.org BioPAX www.biopax.org BOOST www.boost.org cMAP http://cmap.nci.nih.gov CRAN http://cran.r-project.org Entrez http://www.ncbi.nlm.nih.gov/entrez GEO www.ncbi.nlm.nih.gov/geo GO www.geneontology.org The evidence codes: www.geneontology.org/GO.evidence.html Graphviz www.graphviz.org KEGG KEGG: www.kegg.org The dbget archive: www.genome.jp/dbget/dbget.links.html The SOAP API: http://www.genome.ad.jp/kegg/soap libcurl http://curl.haxx.se NAR Nucleic Acids Research on-line category listing http://www3.oup. co.uk/nar/database/c Omegahat http://www.omegahat.org OMIM http://www.ncbi.nlm.nih.gov/Omim PubMed www.ncbi.nlm.nih.gov/entrez R http://www.r-project.org Reactome www.reactome.org Resourcerer http://pga.tigr.org/tigr-scripts/magic/r1.pl W3C http://w3c.org References Affymetrix. Affymetrix Microarray Suite Users Guide. Affymetrix, Santa Clara, CA, version 4.0 edition, 1999a. 19, 20 Affymetrix. 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