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      Differential expression in SAGE: accounting for normal between-library variation.

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          Abstract

          In contrasting levels of gene expression between groups of SAGE libraries, the libraries within each group are often combined and the counts for the tag of interest summed, and inference is made on the basis of these larger 'pseudolibraries'. While this captures the sampling variability inherent in the procedure, it fails to allow for normal variation in levels of the gene between individuals within the same group, and can consequently overstate the significance of the results. The effect is not slight: between-library variation can be hundreds of times the within-library variation.

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          Author and article information

          Journal
          Bioinformatics
          Bioinformatics (Oxford, England)
          Oxford University Press (OUP)
          1367-4803
          1367-4803
          Aug 12 2003
          : 19
          : 12
          Affiliations
          [1 ] Department of Biostatistics, UT M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Box 447, Houston, TX 77030-4009, USA. kabagg@mdanderson.org
          Article
          10.1093/bioinformatics/btg173
          12912827
          7f1c0b04-6edf-455b-800a-7b07d6be28e6
          History

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