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Type: Journal article
Title: Estimating the proportion of microarray probes expressed in an RNA sample
Author: Shi, W.
de Graaf, C.
Kinkel, S.
Achtman, A.
Baldwin, T.
Schofield, L.
Scott, H.
Hilton, D.
Smyth, G.
Citation: Nucleic Acids Research, 2010; 38(7):2168-2176
Publisher: Oxford Univ Press
Issue Date: 2010
ISSN: 0305-1048
Statement of
Wei 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
Abstract: A 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.
Keywords: Thymus Gland
Hematopoietic Stem Cells
Stem Cells
Transcription Factors
Oligonucleotide Probes
RNA, Messenger
Oligonucleotide Array Sequence Analysis
Gene Expression Profiling
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 (, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI: 10.1093/nar/gkp1204
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