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Research Article

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

  • Natalie A. Twine,

    Affiliations: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia, New South Wales Systems Biology Initiative, University of New South Wales, Sydney, New South Wales, Australia

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  • Karolina Janitz,

    Affiliation: Ramaciotti Centre for Gene Function Analysis, University of New South Wales, Sydney, New South Wales, Australia

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  • Marc R. Wilkins,

    Affiliations: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia, New South Wales Systems Biology Initiative, University of New South Wales, Sydney, New South Wales, Australia, Ramaciotti Centre for Gene Function Analysis, University of New South Wales, Sydney, New South Wales, Australia

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  • Michal Janitz mail

    m.janitz@unsw.edu.au

    Affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia

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  • Published: January 21, 2011
  • DOI: 10.1371/journal.pone.0016266

Reader Comments (1)

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Fold change or Ratio?

Posted by Daan on 13 Apr 2012 at 09:00 GMT

Dear Authors.
I'm a bit confused about the fold changes presented in your manuscript.
How is the fold change calculated in tables 3,4 and 5? It seems that they are just ratio's of (FPKM-AD/FPKM-N)?
As an example: if i would calculate the fold change for PCK1 in table 4 according to cufflinks (In (FPKM-AD / FPKM-N)/ In (2) ) i would get a fold change of
In (3.186619/0.121441)/ In (2) = 4.71 instead of 26.24.
If my calculations are true, the results would therefore overrepresent much larger fold changes than are actually true.
Can you please clarify this? Thank you in advance

Greetings
Daan van Abel


No competing interests declared.