About one and a half years ago I wrote a blog post titled “GTEx is throwing away 90% of their data“. The post was, shall we say, “direct”. For example, in reference to the RNA-Seq quantification program Flux Capacitor I wrote that
Using Flux Capacitor is equivalent to throwing out 90% of the data!
I added that “the methods description in the Online Methods of Montgomery et al. can only be (politely) described as word salad” (after explaining that the methods underlying the program were never published, except for a brief mention in that paper). I referred to the sole figure in Montgomery et al. as a “completely useless” description of the method (and showed that it contained errors). I highlighted the fact that many aspects of Flux Capacitor, its description and documentation provided on its website were “incoherent”. Can we agree that this description is not flattering?
The claim about “throwing out 90% of the data” was based on benchmarking I reported on in the blog post. If I were to summarize the results (politely), I would say that the take home message was that Flux Capacitor is junk. Perhaps nobody had really noticed because nobody cared about the program. Flux Capacitor was literally being used only by the authors of the program (and their affiliates, which turned out to include the ENCODE, GENCODE, GEUVADIS and GTEx consortiums). In fact, when I wrote the blog post, I don’t think the program had ever been benchmarked or compared to other tools. It was, after all, unpublished and besides, nobody reads consortium papers. However after I blogged a few others decided to include Flux Capacitor in their benchmarks and the conclusions reached were the same as mine: Flux Capacitor is junk and Flux Capacitor is junk. Of course some people objected to my blog post when it came out, so it’s fun to be right and have others say so in print. But true vindication has come in the form of a citation to the blog post in a published paper in a journal! Specifically, in
C. Iannone, A. Pohl, P. Papasaikas, D. Soronellas, G.P. Vincent, M. Beato and J. Valcárcel, Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells, RNA 21 (2015) 360–374
the authors cite my blog post. They write:
Ummm…. wait… WHAT THE FLUX? The authors actually used Flux Capacitor for their analysis, and are citing my blog at https://liorpachter.wordpress.com/tag/flux-capacitor/ as the definitive reference for the program. Wait, what again?? They used my blog post as a reference for the method??? This is like [[ readers are invited to leave a comment offering a suitable analogy ]].
I’m not really sure what the authors can do at this point. They could publish an erratum and replace the citation. But with what? Flux Capacitor still hasn’t been published (!) Then there is the journal. Does any journal really think it is acceptable to list my blog as the citation for an RNA-Seq quantification tool that is fundamental for the results in a paper? (I’m flattered, but still…) Speaking of the journal, where were the reviewers? How could they not catch this? And the readers? The paper has been out since January… I have to ask: has anybody read it? Of course the biggest embarrassment here is the fact that there is a citation for Flux Capacitor at all. Why on earth are the authors using this discredited program??? Well maybe one answer is to be found in the acknowledgments section, where the group of a PI from the GTEx project is thanked. Actually, this PI was the last author on one of the recently published GTEx companion papers, which, I am sad to say… used Flux Capacitor (albeit with some quantifications performed with Cufflinks as well to demonstrate “robustness”). Why would GTEx be pushing for Flux Capacitor and insist on its use? We’ve come full circle to my GTEx blog post. By now I don’t even know what I think is the most embarrassing part of this whole story. So I thought I’d host a poll: