School of Mathematics and Statistics - Research Publications

Permanent URI for this collection

http://hdl.handle.net/11343/294

Filters

2010 1
1
Reset filters

Settings
Statistics
Citations
Author: ACHTMAN, ARIEL × Author: Hilton, Douglas × Author: Smyth, Gordon × Start date: 2004 ×

Search Results

Now showing 1 - 1 of 1
  • Item
    Thumbnail Image
    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 (OXFORD UNIV PRESS, 2010-04)
    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.