Methodology article
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays
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* Corresponding author: Henrik Bengtsson hb@stat.berkeley.edu
- † Equal contributors
1 Department of Statistics, University of California, Berkeley, USA
2 Bioinformatics Division, Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
BMC Bioinformatics 2010, 11:245 doi:10.1186/1471-2105-11-245
Published: 12 May 2010Additional files
Additional file 1:
Affymetrix GenomeWideSNP_6 data after CRMAv2 preprocessing (sample TCGA-23-1027). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Affymetrix GenomeWideSNP_6 data set preprocessed with the CRMAv2 method.
Format: PDF Size: 1.3MB Download file
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Additional file 2:
Affymetrix GenomeWideSNP_6 data after CRMAv2 preprocessing (sample TCGA-23-1027; with confidence scores). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Affymetrix GenomeWideSNP_6 data set preprocessed with the CRMAv2 method using the SNPs with 90% highest confidence scores.
Format: PDF Size: 1.3MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
Affymetrix GenomeWideSNP_6 data after ismpolish preprocessing (sample TCGA-23-1027). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Affymetrix GenomeWideSNP_6 data set preprocessed with the ismpolish method.
Format: PDF Size: 1.2MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
Affymetrix GenomeWideSNP_6 data after ismpolish preprocessing (sample TCGA-23-1027; with confidence scores). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Affymetrix GenomeWideSNP_6 data set preprocessed with the ismpolish method using the SNPs with 90% highest confidence scores.
Format: PDF Size: 1.2MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 5:
Illumina Human1M-Duo data after BeadStudio,XY preprocessing (sample TCGA-23-1027). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Illumina Human1M-Duo data set preprocessed with the BeadStudio,XY method.
Format: PDF Size: 851KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 6:
Illumina Human1M-Duo data after BeadStudio,XY preprocessing (sample TCGA-23-1027; with confidence scores). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Illumina Human1M-Duo data set preprocessed with the BeadStudio,XY method using the SNPs with 90% highest confidence scores.
Format: PDF Size: 849KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 7:
Illumina Human1M-Duo data after BeadStudio,BAF preprocessing (sample TCGA-23-1027). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Illumina Human1M-Duo data set preprocessed with the BeadStudio,BAF method.
Format: PDF Size: 819KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 8:
Illumina Human1M-Duo data after BeadStudio,BAF preprocessing (sample TCGA-23-1027; with confidence scores). Assessment of TumorBoost based on tumor/normal pair TCGA-23-1027 in the Illumina Human1M-Duo data set preprocessed with the BeadStudio,BAF method using the SNPs with 90% highest confidence scores.
Format: PDF Size: 818KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 9:
Affymetrix GenomeWideSNP_6 data after CRMAv2 preprocessing (sample TCGA-02-0001). Assessment of TumorBoost based on tumor/normal pair TCGA-02-0001 in the Affymetrix GenomeWideSNP_6 data set preprocessed with the CRMAv2 method.
Format: PDF Size: 1.7MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 10:
Affymetrix GenomeWideSNP_6 data after CRMAv2 preprocessing (sample TCGA-02-0001; with confidence scores). Assessment of TumorBoost based on tumor/normal pair TCGA-02-0001 in the Affymetrix GenomeWideSNP_6 data set preprocessed with the CRMAv2 method using the SNPs with 90% highest confidence scores.
Format: PDF Size: 1.7MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 11:
Illumina HumanHap550 data after BeadStudio,XY preprocessing (sample TCGA-02-0001). Assessment of TumorBoost based on tumor/normal pair TCGA-02-0001 in the Illumina HumanHap550 data set preprocessed with the BeadStudio,XY method.
Format: PDF Size: 1.5MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 12:
Illumina HumanHap550 data after BeadStudio,XY preprocessing (sample TCGA-02-0001; with confidence scores). Assessment of TumorBoost based on tumor/normal pair TCGA-02-0001 in the Illumina HumanHap550 data set preprocessed with the BeadStudio,XY method using the SNPs with 90% highest confidence scores.
Format: PDF Size: 1.5MB Download file
This file can be viewed with: Adobe Acrobat Reader