Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
- Resource Type
- Authors
- Van Belle, Werner; Gerits, Nancy; Jakobsen, Kirsti; Brox, Vigdis; Van Ghelue, Marijke; Moens, Ugo
- Source
- Gene Regulation and Systems Biology, Vol 1 (2007)
Gene Regulation and Systems Biology, Vol 1, Pp 57-72 (2007)
Gene Regulation and Systems Biology
- Subject
- VDP::Medisinske Fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710::Medisinsk genetikk: 714
Microarray analysis
downregulation
VDP::Medical disciplines: 700::Basic medical, dental and veterinary science disciplines: 710::Medical genetics: 714
differential expression
Computer Science Applications
lcsh:Biology (General)
Genetics
measurement errors
Molecular Biology
lcsh:QH301-705.5
confidence intervals
upregulation
Ecology, Evolution, Behavior and Systematics
Original Research
gene-array
- Language
- English
- ISSN
- 1177-6250
To perform a quantitative analysis with gene-arrays, one must take into account inaccuracies (experimental variations, biological variations and other measurement errors) which are seldom known. In this paper we investigated amplification and noise propagation related errors by measuring intensity dependent variations. Based on a set of control samples, we create confidence intervals for up and down regulations. We validated our method through a qPCR experiment and compared it to standard analysis methods (including loess normalization and filtering methods based on genetic variability). The results reveal that amplification related errors are a major concern.