title: Technical and biological variance structure in mRNA-Seq data: life in the real world.
abstract: BACKGROUND
  mRNA expression data from next generation sequencing platforms is obtained in the form of counts per gene or exon. Counts have classically been assumed to follow a Poisson distribution in which the variance is equal to the mean. The Negative Binomial distribution which allows for over-dispersion, i.e., for the variance to be greater than the mean, is commonly used to model count data as well.
  
  
  RESULTS
  In mRNA-Seq data from 25 subjects, we found technical variation to generally follow a Poisson distribution as has been reported previously and biological variability was over-dispersed relative to the Poisson model. The mean-variance relationship across all genes was quadratic, in keeping with a Negative Binomial (NB) distribution. Over-dispersed Poisson and NB distributional assumptions demonstrated marked improvements in goodness-of-fit (GOF) over the standard Poisson model assumptions, but with evidence of over-fitting in some genes. Modeling of experimental effects improved GOF for high variance genes but increased the over-fitting problem.
  
  
  CONCLUSIONS
  These conclusions will guide development of analytical strategies for accurate modeling of variance structure in these data and sample size determination which in turn will aid in the identification of true biological signals that inform our understanding of biological systems.
authors: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA. oberg.ann@mayo.edu
authors: Ann L
authors: AL
authors: Oberg
authors: Brian M
authors: BM
authors: Bot
authors: Diane E
authors: DE
authors: Grill
authors: Gregory A
authors: GA
authors: Poland
authors: Terry M
authors: TM
authors: Therneau
mesh_terms: D000293:Adolescent; D000906:Antibodies / Q000235:genetics / Q000378:metabolism; D016010:Binomial Distribution; D002648:Child; D005260:Female; D006801:Humans; D056724:Immunity, Humoral; D015233:Models, Statistical; D016012:Poisson Distribution; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012409:Rubella / Q000517:prevention & control; D012411:Rubella Vaccine / Q000627:therapeutic use; D055815:Young Adult
chemical_list: D000906:Antibodies; D012333:RNA, Messenger; D012411:Rubella Vaccine