Tag Archives: genomics

Mindlessly normalizing genomics data is bad - but ignoring unwanted variability can be worse

Yesterday, and bleeding over into today, quantile normalization (QN) was being discussed on Twitter. This is the tweet that started the whole thing off. The conversation went a bunch of different directions and then this happened: well, this happens all over … Continue reading

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Please save the unsolicited R01s

Editor's note: With the sequestration deadline hours away, the career of many young US scientists is on the line.  In this guest post, our colleague Steven Salzberg , an avid defender of NIH and its peer review process, tells us why now more … Continue reading

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The scientific reasons it is not helpful to study the Newtown shooter's DNA

The Connecticut Medical Examiner has asked to sequence and study the DNA of the recent Newtown shooter. I've been seeing this pop up over the last few days on a lot of popular media sites, where they mention some objections … Continue reading

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Sunday data/statistics link roundup 12/23/12

A cool data visualization for blood glucose levels for diabetic individuals. This kind of interactive visualization can help people see where/when major health issues arise for chronic diseases. This was a class project by Jeff Heer's Stanford CS448B students Ben Rudolph … Continue reading

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Top-down versus bottom-up science: data analysis edition

In our most recent video, Steven Salzberg discusses the ENCODE project. Some of the advantages and disadvantages of top-down science are described.  Here, top-down refers to big coordinated projects like the Human Genome Project (HGP). In contrast, the approach of funding … Continue reading

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Sunday Data/Statistics Link Roundup (9/2/2012)

Just got back from IBC 2012 in Kobe Japan. I was in an awesome session (organized by the inimitable Lieven Clement) with great talks by Matt McCall, Djork-Arne Clevert, Adetayo Kasim, and Willem Talloen. Willem’s talk nicely tied in our … Continue reading

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Replication and validation in -omics studies - just as important as reproducibility

The psychology/social psychology community has made replication a huge focus over the last year. One reason is the recent, public blow-up over a famous study that did not replicate. There are also concerns about the experimental and conceptual design of … Continue reading

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Follow up on "Statistics and the Science Club"

I agree with Roger’s latest post: “we need to expand the tent of statistics and include people who are using their statistical training to lead the new science”. I am perhaps a bit more worried than Roger. Specifically, I worry that talented go-getters … Continue reading

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"How do we evaluate statisticians working in genomics? Why don't they publish in stats journals?" Here is my answer

During the past couple of years I have been asked these questions by several department chairs and other senior statisticians interested in hiring or promoting faculty working in genomics. The main difficulty stems from the fact that we (statisticians working … Continue reading

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Sample mix-ups in datasets from large studies are more common than you think

If you have analyzed enough high throughput data you have seen it before: a male sample that is really a female, a liver that is a kidney, etc… As the datasets I analyze get bigger I see more and more … Continue reading

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