Comments for Reproducible Research Ideas

Comment on Three reasons to distrust microarray results by Software Carpentry » Three Reasons to Distrust Microarray Results

Software Carpentry » Three Reasons to Distrust Microarray Results — Sat, 28 Jan 2012 14:11:59 +0000

[...] Interesting post: …the paper actually demonstrated that is it possible to distinguish microarray experiments conducted on one day from experiments conducted another day. That is, batch effects from the lab were much larger than differences between patients who did and did not respond to therapy… As is so often the case, data were mislabeled. In fact, 3/4 of the samples were mislabeled. [...]

Comment on How to teach RR in one hour by Software Carpentry » Data Provenance Challenge

Software Carpentry » Data Provenance Challenge — Sat, 28 Jan 2012 03:03:53 +0000

[...] summary of our discussion about what to teach scientists about reproducible research if they already believe it’s a good thing, and want to start doing it reminded me that I [...]

Comment on Round table on reproducible research at ICIP 2011 by Take Control of Your Code by Steve Eddins « Reproducible Research Ideas

Take Control of Your Code by Steve Eddins « Reproducible Research Ideas — Fri, 07 Oct 2011 19:42:12 +0000

[...] About « Round table on reproducible research at ICIP 2011 [...]

Comment on Quiet times, busy times by Store-Share-and-Cite: Increase your citations by (re)use of research data « Reproducible Research Ideas

Sun, 21 Aug 2011 18:47:34 +0000

[...] wrote two months ago about the mini-symposium “Store-Share-and-Cite” at TU Delft, where I gave a talk. The [...]

Comment on Three reasons to distrust microarray results by Todd Martinsky

Todd Martinsky — Tue, 09 Aug 2011 19:33:39 +0000

If they use our 2-color platform and dye swap experimental design, that will remove any batch artifacts and false positives.

Comment on Quiet times, busy times by Patrick

Patrick — Mon, 04 Jul 2011 19:06:43 +0000

Thanks for your reaction, Nicolas. The 3TU Data Center is available under http://datacentrum.3tu.nl/en/home/. Not sure whether this is useful to you, as I think it is limited to the 3 Dutch Technical Universities. But connecting initiatives is indeed great already, and can maybe provide an exchange of ideas.

Comment on Quiet times, busy times by nicolas limare

nicolas limare — Mon, 04 Jul 2011 14:26:42 +0000

Could you provide a link to this dataset storage initiative? We (IPOL http://www.ipol.im/) and others (HCI http://hci.iwr.uni-heidelberg.de/ ) might be interested.

Comment on article: Publish your computer code: it is good enough by Igor Carron

Igor Carron — Sat, 14 May 2011 17:50:16 +0000

I wrote something similar:
http://nuit-blanche.blogspot.com/2010/11/nobody-cares-about-you-and-your.html

Comment on Preserving (the memory of) documents by Kevin

Kevin — Fri, 08 Apr 2011 10:19:19 +0000

You say “Preserving the Declaration of Independence is easy; preserving meeting notes is hard”. Surely the problem is preserving the media not the actual information. Even with nitrogen and low lights the document will eventually degrade though it might take thousands of years. On the other hand your photograph of the Rosetta disk will probably be archived many times somewhere on the internet and may even exist at the end of history. I have fossil stromatolites from the period of the first unicelluar life on earth 2 billion years ago. “Information” can exist easily that long but the problem is that we have almost no power to select what will remain and what will be lost – even if it is the Rosetta Stone or the Declaration of Independence.

Comment on article: Publish your computer code: it is good enough by reproducible research with R // sos4R

reproducible research with R // sos4R — Mon, 10 Jan 2011 12:48:05 +0000

[...] A column in Nature magazine: “Publish your computer code: it is good enough” (via rr.net) [...]