Seq-ing improved gene expression estimates from microarrays using machine learning.
BACKGROUND
Quantifying gene expression by RNA-Seq has several advantages over microarrays, including greater dynamic range and gene expression estimates on an absolute, rather than a relative scale. Nevertheless, microarrays remain in widespread use, demonstrated by the ever-growing numbers of samples deposited in public repositories.


RESULTS
We propose a novel approach to microarray analysis that attains many of the advantages of RNA-Seq. This method, called Machine Learning of Transcript Expression (MaLTE), leverages samples for which both microarray and RNA-Seq data are available, using a Random Forest to learn the relationship between the fluorescence intensity of sets of microarray probes and RNA-Seq transcript expression estimates. We trained MaLTE on data from the Genotype-Tissue Expression (GTEx) project, consisting of Affymetrix gene arrays and RNA-Seq from over 700 samples across a broad range of human tissues.


CONCLUSIONS
This approach can be used to accurately estimate absolute expression levels from microarray data, at both gene and transcript level, which has not previously been possible. This methodology will facilitate re-analysis of archived microarray data and broaden the utility of the vast quantities of data still being generated.
School of Biochemistry and Cell Biology, University College Cork, Western Road, Cork, Ireland. paul.korir@gmail.com.
Paul K
PK
Korir
Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL-60637, USA. paul.geeleher@gmail.com.
Paul
P
Geeleher
School of Mathematics, Statistics and Applied Mathematics, University Road, Galway, Ireland. cathal.seoighe@nuigalway.ie.|Institute of Infectious Disease and Molecular Medicine, Anzio Road, Cape Town, 7925, South Africa. cathal.seoighe@nuigalway.ie.
Cathal
C
Seoighe
D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D000069550:Machine Learning / Q000592:standards*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome