Literature-based evaluation of microarray normalization procedures

Nicholas A. Furlotte, Lijing Xu, Robert Williams, Ramin Homayouni

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

Normalization procedures attempt to remove non-biological variance found within micro array datasets. The choice of normalization procedure is important, as it has a dramatic effect on downstream data analysis. Although many normalization procedures have been developed, comparison and evaluation of their performance is difficult. We present a method to evaluate normalization procedures by utilizing gene-gene associations derived from the biomedical literature via Latent Semantic Indexing. The functional coherence of co-regulated genes obtained from different normalized data sets is calculated in order to evaluate the effectiveness of each normalization procedure. The method was tested on three popular normalization procedures (MAS5, PDNN and RMA) applied to gene expression across 71 recombinant inbred mouse brain samples. Results show that, on average, MAS5 outperforms both PDNN and RMA by producing a higher number of functionally cohesive gene sets. These results demonstrate that our literature-based cohesion analysis can provide an objective method for evaluation of normalization procedures.

Original languageEnglish (US)
Title of host publicationProceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011
Pages608-612
Number of pages5
DOIs
StatePublished - Dec 1 2011
Event2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Other

Other2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Fingerprint

Microarrays
Genes
Gene expression
Brain
Semantics
Gene Expression

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Furlotte, N. A., Xu, L., Williams, R., & Homayouni, R. (2011). Literature-based evaluation of microarray normalization procedures. In Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011 (pp. 608-612). [6120512] https://doi.org/10.1109/BIBM.2011.114

Literature-based evaluation of microarray normalization procedures. / Furlotte, Nicholas A.; Xu, Lijing; Williams, Robert; Homayouni, Ramin.

Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. p. 608-612 6120512.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Furlotte, NA, Xu, L, Williams, R & Homayouni, R 2011, Literature-based evaluation of microarray normalization procedures. in Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011., 6120512, pp. 608-612, 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBM.2011.114
Furlotte NA, Xu L, Williams R, Homayouni R. Literature-based evaluation of microarray normalization procedures. In Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. p. 608-612. 6120512 https://doi.org/10.1109/BIBM.2011.114
Furlotte, Nicholas A. ; Xu, Lijing ; Williams, Robert ; Homayouni, Ramin. / Literature-based evaluation of microarray normalization procedures. Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. pp. 608-612
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