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Estimating the proportion of microarray probes expressed in an RNA sample

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dc.contributor.authorShi, W.
dc.contributor.authorde Graaf, C.
dc.contributor.authorKinkel, S.
dc.contributor.authorAchtman, A.
dc.contributor.authorBaldwin, T.
dc.contributor.authorSchofield, L.
dc.contributor.authorScott, H.
dc.contributor.authorHilton, D.
dc.contributor.authorSmyth, G.
dc.date.issued2010
dc.description.abstractA fundamental question in microarray analysis is the estimation of the number of expressed probes in different RNA samples. Negative control probes available in the latest microarray platforms, such as Illumina whole genome expression BeadChips, provide a unique opportunity to estimate the number of expressed probes without setting a threshold. A novel algorithm was proposed in this study to estimate the number of expressed probes in an RNA sample by utilizing these negative controls to measure background noise. The performance of the algorithm was demonstrated by comparing different generations of Illumina BeadChips, comparing the set of probes targeting well-characterized RefSeq NM transcripts with other probes on the array and comparing pure samples with heterogenous samples. Furthermore, hematopoietic stem cells were found to have a larger transcriptome than progenitor cells. Aire knockout medullary thymic epithelial cells were shown to have significantly less expressed probes than matched wild-type cells.
dc.description.statementofresponsibilityWei Shi, Carolyn A. de Graaf, Sarah A. Kinkel, Ariel H. Achtman, Tracey Baldwin, Louis Schofield, Hamish S. Scott, Douglas J. Hilton and Gordon K. Smyth
dc.identifier.citationNucleic Acids Research, 2010; 38(7):2168-2176
dc.identifier.doi10.1093/nar/gkp1204
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.orcidScott, H. [0000-0002-5813-631X]
dc.identifier.urihttp://hdl.handle.net/2440/61364
dc.language.isoen
dc.publisherOxford Univ Press
dc.relation.granthttp://purl.org/au-research/grants/nhmrc/490037
dc.rights© The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttps://doi.org/10.1093/nar/gkp1204
dc.subjectThymus Gland
dc.subjectHematopoietic Stem Cells
dc.subjectStem Cells
dc.subjectAnimals
dc.subjectMice
dc.subjectTranscription Factors
dc.subjectOligonucleotide Probes
dc.subjectRNA, Messenger
dc.subjectOligonucleotide Array Sequence Analysis
dc.subjectGene Expression Profiling
dc.subjectAlgorithms
dc.subjectAIRE Protein
dc.titleEstimating the proportion of microarray probes expressed in an RNA sample
dc.typeJournal article
pubs.publication-statusPublished

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