Pro-MAP: a robust pipeline for the pre-processing of single channel protein microarray data

Metoboroghene Oluwaseyi Mowoe, Shaun Garnett, Katherine Lennard, Jade Talbot, Paul Townsend, Eduard Jonas, Jonathan Michael Blackburn

Research output: Contribution to journalArticlepeer-review


BACKGROUND: The central role of proteins in diseases has made them increasingly attractive as therapeutic targets and indicators of cellular processes. Protein microarrays are emerging as an important means of characterising protein activity. Their accurate downstream analysis to produce biologically significant conclusions is largely dependent on proper pre-processing of extracted signal intensities. However, existing computational tools are not specifically tailored to the nature of these data and lack unanimity.

RESULTS: Here, we present the single-channel Protein Microarray Analysis Pipeline, a tailored computational tool for analysis of single-channel protein microarrays enabling biomarker identification, implemented in R, and as an interactive web application. We compared four existing background correction and normalization methods as well as three array filtering techniques, applied to four real datasets with two microarray designs, extracted using two software programs. The normexp, cyclic loess, and array weighting methods were most effective for background correction, normalization, and filtering respectively.

CONCLUSIONS: Thus, here we provided a versatile and effective pre-processing and differential analysis workflow for single-channel protein microarray data in form of an R script and web application ( .) for those not well versed in the R programming language.

Original languageEnglish
Article number534
Pages (from-to)534
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 9 Dec 2022


  • Microarray
  • Pro-MAP
  • Protein
  • Protein microarray analysis
  • Single channel

Research Beacons, Institutes and Platforms

  • Manchester Cancer Research Centre


Dive into the research topics of 'Pro-MAP: a robust pipeline for the pre-processing of single channel protein microarray data'. Together they form a unique fingerprint.

Cite this