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Motif effects in Affymetrix GeneChips seriously affect probe intensities
Graham J G Upton1, Andrew P Harrison
1Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK. gupton@essex.ac.uk
Nucleic Acids Research
|August 21, 2012
Summary
Gene expression analysis using Affymetrix GeneChips is affected by probe sequence. This study reveals significant variations in probe values due to sequence, impacting gene expression data interpretation.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Affymetrix GeneChips measure gene expression using probe values.
- Probe values are assumed to reflect gene expression levels accurately.
Purpose of the Study:
- To investigate the influence of probe base sequence on Affymetrix GeneChip probe values.
- To identify sequence-dependent effects impacting gene expression data.
Main Methods:
- Analysis of over 28,000 CEL files across 10 Affymetrix GeneChip platforms.
- Statistical examination of probe values in relation to their base sequences.
Main Results:
- Probe values are significantly influenced by their specific base sequences.
- Confirmed known sequence effects (T7-primer, G-quadruplexes) and identified novel sequence-related variations.
- Demonstrated substantial variability in probe values across experiments, batches, and CEL files.
Conclusions:
- Base sequence is a critical factor affecting Affymetrix GeneChip probe values.
- Sequence-dependent variations can introduce significant noise and bias into gene expression data.
- Careful consideration of probe sequence effects is necessary for accurate gene expression analysis.
