“Investigating the compliance of our publications with MIAME standards (minimum information about a microarray experiment; Editorial, ”https://www.nature.com/ng/journal/v38/n10/full/ng1006-1089.html">Nat. Genet. 38, 1089; 2006), we found that even when authors and referees are aware of community standards and even with editors mandating both data deposition and accession linking as a condition of publication, a proportion of microarray datasets were at that time unavailable or incomplete." So starts the Editorial in this month’s (February issue) Nature Genetics (41, 135; 2009).

In an Analysis article in the same issue of the journal (Nat. Genet. 41, 149-155; 2009), John P. A. Ioannidis and collaborators (four teams) treated the findings of a number of microarray papers published in Nature Genetics between 2005 and 2006 as their gold standard, and attempted to replicate a sample of the analyses conducted on each of them, with frankly dismal results.

According to the Editorial, “the findings of this Analysis should be used to improve practice rather than to critize the authors and referees of these publications. A certain amount of both skepticism and initiative must of course be assumed on behalf of all readers and users of research publications. Equally, there must be enough goodwill and professionalism in the research community to permit critical reanalysis of research findings at any and every moment without this core scientific practice implying any personal criticism. Any scientist should be prepared to reexamine published work, one’s own and one’s colleagues’ alike. In doing so it always helps to make clear one’s needs and assumptions, and the Analysis in this issue does indeed explain the limits of the analysts’ requirements and critical aims.”

The journal, and other Nature journals that publish papers describing microarrays, now insist that authors deposit their data to GEO or ArrayExpress before the submitted paper is sent for peer-review.

Nature journals’ policies on data and materials availability, including microarray deposition.

MGED website, specifying MIAME standards necessary to interpret and reproduce microarray data.