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Series GSE23682 Query DataSets for GSE23682
Status Public on Jun 09, 2011
Title Removing System Noise from Comparative Genomic Hybridization Data by Self-Self Analysis
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary To minimize the distortion of genetic signal by system noise, we have explored the latter in an archive of hybridizations in which no genetic signal is expected. This archive is obtained by comparative genomic hybridization (CGH) of a reference sample in one channel to the same sample in the other channel, which we have termed ‘self-self’ data. We show that these self-self hybridizations trap a variety of system noise inherent in sample-reference (test) data. Through singular value decomposition (SVD) of self-self data, we are able to determine the principal components of system noise. Assuming simple linear models of noise generation, we present evidence that the linear correction of test data with self-self data—which we call system normalization—reduces local and long-range correlations as well as improves signal-to-noise metrics, yet does not introduce detectable spurious signal.
 
Overall design 132 self-self hybridizations which should not have any genomic signal, and 3720 test hybridizations done against reference genome CSHL0001.
 
Contributor(s) Wigler M, Lee Y
Citation(s) 21658583, 21658582, 22207624
Submission date Aug 18, 2010
Last update date Mar 22, 2012
Contact name Yoon-Ha Lee
E-mail leey@cshl.edu
Organization name Cold Spring Harbor Lab
Street address One Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platforms (1)
GPL10815 NimbleGen Human 2.1M array [080131_HG18_WG_CGH_v2DCR_HX1]
Samples (3852)
GSM581053 GM10851_NG01906
GSM581054 GM10851_NG01907
GSM581055 GM10851_NG01908
Relations
BioProject PRJNA130799

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
GSE23682_RAW.tar 385.1 Gb (http)(custom) TAR (of PAIR, TXT)
GSE23682_eigenVector_Data.tar.gz 193.9 Mb (ftp)(http) TAR
GSE23682_family_table.txt.gz 29.0 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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