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Updated: Jun 6, 2026

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
Published on: September 18, 2021
Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
Leo Lahti1, Laura L Elo, Tero Aittokallio
1Helsinki Institute for Information Technology, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto, Finland. leo.lahti@iki.fi
Abstract:
Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we introduce and validate a targeted probabilistic method for analyzing probe reliability directly from expression data and independently of the noise source. This provides insights into the various sources of probe-level noise and gives tools to guide probe design.
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