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1 Package PREDAsampledata July 17, 2013 Title expression and copy number data on clear cell renal carcinoma samples Version Author I. Cifola et al. in Cristina Battaglia Lab, University of Milan Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) Depends R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate,gahgu133plus2.db, gahgu133plus2cdf Suggests hgu133plus2.db, hgu133plus2cdf Maintainer Francesco Ferrari <francesco.ferrari@unimore.it> License Artistic-2.0 biocviews ExperimentData, Cancer R topics documented: AffybatchRCC ExpressionSetRCC gaexpressionsetrcc GEanalysisResults SODEGIRCNanalysisResults SODEGIRCNDataForPREDA SODEGIRGEanalysisResults SODEGIRGEDataForPREDA Index 8 1
2 2 ExpressionSetRCC AffybatchRCC AffyBatch object for clear cell renal carcinoma (RCC) sample dataset An AffyBatch object containint raw data from clear cell renal carcinoma (RCC) dataset CEL files data(affybatchrcc) The sample gene expression dataset includes 12 samples of clear cell renal carcinoma and 11 samples from normal kidney tissue. Ingrid Cifola, Roberta Spinelli, Luca Beltrame, Clelia Peano, Ester Fasoli, Stefano Ferrero, Silvano Bosari, Stefano Signorini, Francesco Rocco, Roberto Perego, Vanessa Proserpio, Francesca Raimondo, Paolo Mocarelli, and Cristina Battaglia. Genomewide screening of copy number alterations and loh events in renal cell carcinomas and integration with gene expression profile. Mol Cancer, 7:6, data(affybatchrcc) AffybatchRCC ExpressionSetRCC ExpressionSet object for clear cell renal carcinoma (RCC) sample dataset An ExpressionSet object containint justrma preprocessed data for clear cell renal carcinoma (RCC) dataset, using standard Affymetrix CDF data(expressionsetrcc)
3 gaexpressionsetrcc 3 The sample gene expression dataset includes 12 samples of clear cell renal carcinoma and 11 samples from normal kidney tissue. Ingrid Cifola, Roberta Spinelli, Luca Beltrame, Clelia Peano, Ester Fasoli, Stefano Ferrero, Silvano Bosari, Stefano Signorini, Francesco Rocco, Roberto Perego, Vanessa Proserpio, Francesca Raimondo, Paolo Mocarelli, and Cristina Battaglia. Genomewide screening of copy number alterations and loh events in renal cell carcinomas and integration with gene expression profile. Mol Cancer, 7:6, data(expressionsetrcc) ExpressionSetRCC gaexpressionsetrcc ExpressionSet object for clear cell renal carcinoma (RCC) sample dataset based on GeneAnnot custom CDF An ExpressionSet object containint justrma preprocessed data for clear cell renal carcinoma (RCC) dataset, using GeneAnnot based custom CDF (gahgu133plus2cdf). data(expressionsetrcc) The sample gene expression dataset includes 12 samples of clear cell renal carcinoma and 11 samples from normal kidney tissue.
4 4 GEanalysisResults Ingrid Cifola, Roberta Spinelli, Luca Beltrame, Clelia Peano, Ester Fasoli, Stefano Ferrero, Silvano Bosari, Stefano Signorini, Francesco Rocco, Roberto Perego, Vanessa Proserpio, Francesca Raimondo, Paolo Mocarelli, and Cristina Battaglia. Genomewide screening of copy number alterations and loh events in renal cell carcinomas and integration with gene expression profile. Mol Cancer, 7:6, data(gaexpressionsetrcc) gaexpressionsetrcc GEanalysisResults RCC gene expression sample dataset - PREDA analysis results PREDA analysis results of RCC gene expression sample dataset. The PREDA analysis was focused on the detection of differentially expressed genomic regions in tumor samples comparet to normal kidney cells. data(geanalysisresults) data(geanalysisresults) str(geanalysisresults)
5 SODEGIRCNanalysisResults 5 SODEGIRCNanalysisResults SODEGIR analysis results on Copy Number data PREDAResults object containing SODEGIR analysis results on Copy Number data data(sodegircnanalysisresults) See also vignette from PREDA package Copy number data data were obtained from ArrayExpress datasets E-TABM-283/E-TABM Silvio Bicciato, Roberta Spinelli, Mattia Zampieri, Eleonora Mangano, Francesco Ferrari, Luca Beltrame, Ingrid Cifola, Clelia Peano, Aldo Solari, and Cristina Battaglia. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. Nucleic Acids Res, 37(15): , August data(sodegircnanalysisresults) str(sodegircnanalysisresults) SODEGIRCNDataForPREDA Copy Number input data for PREDA analysis DataForPREDA object containing Copy Number input data for PREDA analysis data(sodegircndataforpreda)
6 6 SODEGIRGEanalysisResults See also vignette from PREDA package Copy number data data were obtained from ArrayExpress datasets E-TABM-283/E-TABM Silvio Bicciato, Roberta Spinelli, Mattia Zampieri, Eleonora Mangano, Francesco Ferrari, Luca Beltrame, Ingrid Cifola, Clelia Peano, Aldo Solari, and Cristina Battaglia. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. Nucleic Acids Res, 37(15): , August data(sodegircndataforpreda) str(sodegircndataforpreda) SODEGIRGEanalysisResults SODEGIR analysis results on Gene Expression data PREDADataAndResults object containing SODEGIR analysis results on Gene Expression data data(sodegirgeanalysisresults) See also vignette from PREDA package Silvio Bicciato, Roberta Spinelli, Mattia Zampieri, Eleonora Mangano, Francesco Ferrari, Luca Beltrame, Ingrid Cifola, Clelia Peano, Aldo Solari, and Cristina Battaglia. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. Nucleic Acids Res, 37(15): , August 2009.
7 SODEGIRGEDataForPREDA 7 data(sodegirgeanalysisresults) str(sodegirgeanalysisresults) SODEGIRGEDataForPREDA Gene Expression input data for PREDA analysis DataForPREDA object containing Gene Expression input data for PREDA analysis data(sodegirgedataforpreda) See also vignette from PREDA package Silvio Bicciato, Roberta Spinelli, Mattia Zampieri, Eleonora Mangano, Francesco Ferrari, Luca Beltrame, Ingrid Cifola, Clelia Peano, Aldo Solari, and Cristina Battaglia. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. Nucleic Acids Res, 37(15): , August data(sodegirgedataforpreda) str(sodegirgedataforpreda)
8 Index Topic datasets AffybatchRCC, 2 ExpressionSetRCC, 2 gaexpressionsetrcc, 3 GEanalysisResults, 4 SODEGIRCNanalysisResults, 5 SODEGIRCNDataForPREDA, 5 SODEGIRGEanalysisResults, 6 SODEGIRGEDataForPREDA, 7 AffybatchRCC, 2 ExpressionSetRCC, 2 gaexpressionsetrcc, 3 GEanalysisResults, 4 SODEGIRCNanalysisResults, 5 SODEGIRCNDataForPREDA, 5 SODEGIRGEanalysisResults, 6 SODEGIRGEDataForPREDA, 7 8
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