← BioTransfer GEO Dataset Finder
GEO series

Removing System Noise from Comparative Genomic Hybridization Data by Self-Self Analysis

GSE23682 Homo sapiens Genome variation profiling by genome tiling array 3852 samples Submitted 2011/06/09 Platform GPL10815
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.
This dataset
Download

Direct links to NCBI, no account and no request form: the whole study as GSE23682_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 3852 samples.

Also filed as BioProject PRJNA130799. Searching any of these in the dataset finder brings you back here.

Samples in this study

The sample list for this study is not cached yet. Press Sort into groups and it will be fetched from NCBI.

+ 3852 more — browse all 3852 samples with per-sample file links →

Similar datasets

Search all human datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.