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Series GSE26075 Query DataSets for GSE26075
Status Public on Dec 16, 2010
Title Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays and 16 ovarian tumors on 500K SNP arrays
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays

Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array.

Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays

Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array.
 
Overall design Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).

Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time. One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. For Chromosome X, the average of the 20 normal female samples was used. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).
 
Contributor(s) Modrusan Z, Neve R, Haverty P, Liu J, Wertz I
Citation(s) 21368834
Submission date Dec 15, 2010
Last update date Dec 22, 2017
Contact name Jinfeng Liu
E-mail(s) liu.jinfeng@gene.com
Organization name Genentech Inc.
Department Bioinformatics and Computational Biology
Street address 1 DNA Way, MS93
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platforms (4)
GPL2004 [Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array
GPL2005 [Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (104)
GSM640202 HF-16897-(1)_Hind
GSM640203 HF-16899-(1)_Hind
GSM640204 HF-16901-(1)_Hind
Relations
BioProject PRJNA135205

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE26075_RAW.tar 1.8 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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