“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.

In a Correspondence to Nature Methods (5, 991; December 2008) responding to an Editorial in the March 2008 issue of the journal (Nat. Meth. 5, 209; 2008) , Scott A Ochsner, David L Steffen, Christian J Stoeckert, Jr and Neil J McKenna report a study showing that researchers are not routinely depositing supporting raw microarray datasets into a public database.

The Correspondence authors surveyed papers from the 2007 issues of 20 journals, searching the text for reference to deposition of a microarray dataset. They find that the rate of deposition of datasets was less than 50 per cent. The authors note the effort required by authors to deposit these complex data in public microarray repositories, even though repositories are simplifying submissions while encouraging compliance with MIAME (minimum information about a microarray experiment) standards. They write: “Although microarray datasets are most useful to bioinformaticians in their raw, unnormalized forms, which facilitate cross-comparison with other datasets, processed datasets are more useful to the bench scientist. Moreover, unless a description of the experimental details is available, neither form of the data are biologically interpretable.” They urge repositories to require deposition by authors and propose journals require a statement in the manuscript identifying a repository and accession number at the time of submission, with the record embargoed until acceptance of the paper. (Of the 16 Nature journal papers that were part of the survey, such accession numbers were provided in 15 cases.) They conclude: “Seven years after the elaboration of the MIAME principles, the emerging discipline of microarray meta-analysis, exemplified by the cancer gene expression resource ”https://www.oncomine.org/“>Oncomine, continues to be hobbled by the mundane, time-consuming and often fruitless exercise of tracking down annotated full datasets. We call for a renewed collective effort from researchers, publishers and funding organizations to redress this situation and secure these data-rich research resources for posterity.”

The full text of the Nature Methods Correspondence, with supporting data, is here.

Policy note: the Nature journals have for some years required authors to submit MIAME-compliant microarray data to the GEO or Arrayexpress public repository. Details of the journals’ polices can be found here.

‘Data not shown’ is an outdated caveat that obscures the transparency of a scientific report and weakens the peer review process, according to Nature Chemical Biology (4, 575; 2008).

“Technology and competition perpetually raise the bar for the quality and quantity of experimental data that authors must include to publish a high-impact manuscript. Almost uniformly, journals have amended their formats to accommodate the increased volume of data while maintaining page restrictions by providing the supplementary information option online for authors and readers. Despite these changes, many authors still rely on the caveat of ‘data not shown’. At Nature Chemical Biology, we discourage the use of this phrase and the omission of important data for two major reasons. First, the exclusion of essential data undermines the peer review process, and second, readers need access to data to form independent opinions about and to replicate the results of published papers. Thus, we suggest that the time for ‘data not shown’ has passed.”

Read the rest of this Editorial here.

For additional details on presenting and consolidating methods, see the journal’s Guide to Authors.

See the NPG authors’ and referees’ website for more details on our data sharing and database deposition policies.