Interpreting ‘omics: a good example this time

Remember how I complained that people often seem to forget the scientific method when it comes to transcriptomics? Well, I’m glad to say some scientists still remember those all-important steps between data and conclusion. When looking at the predicted functions of the genes active in these cute little baby worms* during the first three days of their lives, Kenny and Shimeld (2012) not only compared their data to a “background” dataset from a well-studied animal, but also

  • did statistical tests to confirm that the differences they saw were real,
  • discussed several possible causes for them.

… including those that weren’t biologically interesting at all, like limitations of their methods. In the end, they couldn’t really draw strong conclusions from this particular part of their analysis, but the best thing is they sound perfectly aware of the difficulty and careful not to go too far in interpretation.

Folks, this is how you should write a transcriptomics paper. Not look at a few out-of-context numbers and concoct a story around them.
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*Okay, am I the only one who finds trochophores adorable? :$

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Reference:

Kenny NJ & Shimeld SM (2012) Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida: Serpulidae) reveals annelid trochophore transcription factor cassette. Development Genes & Evolution Online First™ article available online 8/10/2012, doi: 10.1007/s00427-012-0416-6

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