Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments.

ABSTRACT:

Background

Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR) and individual or pooled breast-tumour RNA.

Results

A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amoun

SUBMITTER: Kitchen RR 

PROVIDER: S-EPMC3269440 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature