Estimating the proportion of microarray probes expressed in an RNA sample
- Shi, W; de Graaf, CA; Kinkel, SA; Achtman, AH; Baldwin, T; Schofield, L; Scott, HS; Hilton, DJ; Smyth, GK;
Publication Year 2010-04, Volume 38, Issue #7, Page 2168-2176
- Journal Title
- NUCLEIC ACIDS RESEARCH
- Publication Type
- Journal Article
- 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.
- OXFORD UNIV PRESS
- PROMISCUOUS GENE-EXPRESSION; THYMIC EPITHELIAL-CELLS; STEM-CELLS; LEVEL DATA; AIRE; SELF; NORMALIZATION; AUTOIMMUNITY; PROGENITORS; PHENOTYPE
- Publisher's Version
- Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2010-04-01 12:00:00Last Modified: 0001-01-01 12:00:00