This Monday last year was my first day on the job as a PhD candidate. I settled into my office, got to know people, tried to get all the papers in order and to understand what I should really be doing here. I have now completed 1/3 of my time here and I am quite sure I have not completed 1/3 of the work of my PhD. That’s probably the only thing I can be absolutely sure of. It’s not that I haven’t done things, I’m just training and practicing and then you’re not very efficient.

In a week I will (hopefully) have completed 25 of the 30 credits I need and in three weeks I will have even more results from the transition disequilibrium test ready for my supervisor group. I really like working right now, because my days are varied, what is do is interesting and I know what to do, I just need to figure out how. And I guess that this “treasure hunt” for methods and being clever is what I really like about research. That you have to use everything you know and be super smart to do really good research.

Many things have changed the last year, but the two most important things are still the same, my passions at work and in love. The next year I will have to work on the first two of in total three manuscripts that will become my thesis, so there are many things to look forward to and to aim at. Still a lot go get done and find out.

Imagine a whole year in the same place with the same people and the same daily rhythm. It’s the good live, I tell you.

Okey, so this is how far I have come on my plot. This is just a cropped version of the total plot, each column is a chromosome and where the points (SNPs or genetic marker) are placed along the y-axis depends on their significance. The ones under the red line are the actual significant ones.

I still have a lot to improve and still so many different things I will try with the data, but this is a step in the right direction.

PS: did you see the chess game yesterday? It was fantastic! So exiting! And we will see in just a couple of hours if we today will have the first Norwegian World Champion of Chess 🙂

This is what I have been trying to make the last week, a scatterplot a bit more fancy than this. I have 22 chromosomes (not three species), and I want a horizontal line to indicate significance. But as I have never done any work in R until now (except for courses) this is going a bit slow.

In addition to that there is a group project and presentation in two weeks and a 10 credit course exam in 2,5 weeks. Am I getting nervous? Or working late almost every day? Indeed.

I think we all should know more about false discovery rate and type 2 error.

Do you know this graph? It shows the balance between type 1 (incorrect rejection of a true null hypothesis) and type 2 (failure to reject false null hypothesis) error in statistics. Imagine you have done an analysis to see if any of your genetic markers are connected with the gene you are looking for. When you decide your cut off value (or where you p-value should be), you actually decide the balance you are willing to accept between type 1 and type 2 error.

You see, if you decide that you want a cut off value of 0.05, that might mean that you get 14 significant results (the blue ones in the graph). But that will also mean that there are 18 significant results you didn’t find (the red) because you were too afraid of any of your blue results to be a false positive (a significant result from chance and not actually from the data).

This isn’t so difficult when you do simple tests, but if you do very many tests, the problem increases. And right now at work, I am facing the problem of this after 4500 tests. How do I find a good cut off value so I actually find the significant results, but can trust that they are true positives?

I will keep you updated.

This is my life plan. This is what I will be doing the next 2.5 years. I am the top line and Nicky is the bottom one. You probably don’t understand what it means, but the important bits are:

• I will try to submit my first manuscript in June 2014.
• I will try to submit my second one in September 2014.
• Then I will a whole year to work on my last manuscript before my defence in December 2015.

This autumn I still have 15 credits to finish in addition to the analyses I’m doing, so you can see I am happy I didn’t become troop leader in Longship or committed to anything else. I still have Komité Speiding and a couple (five) projects there, but none of them will finish before Christmas, so I’m good. And there is only 1.5 weeks until the house warming party, so not much left of fixing the apartment either.

Today I am working from home to finish the two presentations I will hold tomorrow. For 5 credits I will talk about animal genetic data analysis (but mostly just genome-wide association studies) and Bayesian statistics and Markov chain Monte Carlo methods in statistical genetics.

It will be my first presentation at UMB and I have fingers and toes crossed that it will be ok. Excited to see if anyone else than my supervisors and the sensor will attend.

But there is still a lot of presentation to finish and some talking to rehearse.

And this weekend I am going to Leikvinjar scout sentre at Hønefoss for a weekend meeting with my comittee and in just two weeks we will have our house warming party!

9/36 is 0.25, that is 25%.

Why is this interesting? Today I have been a PhD candidate for exactly 9 months out of my total of 36. That means that I have already completed 25 % of the PhD.

This makes me a tiny bit stressed.