Tuesday, November 13, 2007
Yesterday, I was using a contributed package in R that requires the access to R's temp directory. The exact location of this folder can be found out using the command tempdir(). It just happened that my current location of this folder was not ideal for the task at hand and I needed to change it. There was no command in R to change it. I figured out a way to do it: add an entry to the environmental variable list of the system as TMPDIR and specify the desired folder name.
Monday, November 12, 2007
Friday, November 02, 2007
return(table(c(x.r, temp.mat[,1]), c(sample(x.c),temp.mat[,2])) -matrix(1, nrow(x), ncol(x)))
I also made a function to do the permutation for each line of my huge
matrix and used the apply() function to speed up things. It works pretty well
Wednesday, October 24, 2007
I found this claim is a little far-fetch. According to scientists, the temperature change due to global warming is about (1.33 ± 0.32 °F) during the last 100 years. The difference between the average temperature of New Jersey and that of a tropical region is probably much greater than that. To me, one possible reason why a single disease is moving north can be genetic mutation in the virus strand that increases cold-resistance. And more frequent air travel can probably explain the trend that multiple diseases have been moving north.
Before having more data, one cannot conclude global warming as the cause and ignore other possible threatening causes.
Monday, September 17, 2007
Sunday, September 16, 2007
Friday, September 07, 2007
Yesterday, I received an email regarding a computational biology challenge. The contestants are supposed to analyze the data and discover the gold standard genes or gene-gene interactions hidden in the data. This is a blinded challenge and the results will be announced during the conference. A winner will be named.
I was intrigued. For a couple of the challenges, I thought of some ideas. I thought, my methods might actually work well. "Shall I enter this contest then?" I asked myself. Then, it suddenly worried me that what if the data do not agree with my assumptions for my method. "That would really be a problem!" I thought, "and I might be at the bottom of the contest." But then it hit me: it would actually be nice that the method doesn't work and we understand which assumptions are wrong. How else can we learn about the biological systems if we don't fail?
This reminded me of my struggle with a simulation study recently. Part of the phenomenon I observed does not agree with my intuition. At first, I kept debugging my codes. But the codes were so short that I was finally convinced that what I observed was a true phenomenon of the statistics I was evaluating when the dimension is too large.
Often, I judge the validity of a method first by intuition. These recent experiences show that knowledge can actually occur when the intuition fails. And intuition is just knowledge based on past failed judgements. Therefore, Chairman Mao was right about one thing, if we don't just do it and fail, we can't learn the truth. Sometimes, it is necessary to make a fool out of ourselves for the greater good---better knowledge for the mankind. :) Or we can just have one more reason to feel less grumpy whenever we fail.
Friday, May 25, 2007
Of course, it is not as simple as it sounds. The reason why the Cell Chip can be faster for high performance computing is its well-designed structure. I am not equipped with the right knowledge to explain this. It is said to be an IBM PowerPC processor with eight vector processor. I can only assume this means better paralell capacity and better efficiency in dealing with high volume computation. Therefore, it takes *VERY* professional programming to take advantage of its power. Until R was programmed to take advantage of such chips, I will keep my eyes on those Core Duo Quad chips.
Tuesday, May 22, 2007
Monday, May 14, 2007
Celebrating Mother's day (i.e., buy gifts ... )
Who do you plan to buy a Mother's Day gift for this
year? (Check all that apply)
(in the order of all, men, women)
Mother or Stepmother
65.2% 64.9% 65.3%
19.4% 39.8% ---
8.4% 4.9% 11.6%
7.4% 6.6% 8.0%
5.3% 3.9% 6.6%
5.7% 4.0% 7.2%
1.1% 0.8% 1.3%
10.7% 5.5% 15.4%
Wednesday, May 09, 2007
- 48% believed in God
- 13% believed in Evolution (God is not involved)
It was then concluded that we are living in a divided country.
I was confused ("confused" is the mostly used words during my office hours) by how the options are organized. Should there be
- believed in God (no evolution)
- believed in God (evolution exists as part of God's plan)
- believed in Evolution (God is involved)
- believed in Evolution (There is God but God is not involved)
- believed in Evolution (There is no God)
It may turns out not to be very divided at all with most of the percentage splitted among the middle options and only small percentages in the two extreme views.
Monday, April 30, 2007
- Bourne PE (2005) Ten simple rules for getting published. PLoS Comp Biol 1: e57.
- Bourne PE, Chalupa LM (2006) Ten simple rules for getting grants. PLoS Comp Biol 2: e12.
- Bourne PE, Korngreen A (2006) Ten simple rules for reviewers. PLoS Comp Biol 2: e110.
- Bourne PE, Friedberg I (2006) Ten simple rules for selecting a postdoctoral fellowship. PLoS Comp Biol 2: e121.
- Vicens Q, Bourne PE (2007) Ten simple rules for a successful collaboration. PLoS Comp Biol 3: e44.
It just published a new set of rules for oral presentations.
Sunday, April 29, 2007
Below is the 10 most common passwords published in PC magazine on April 18, 2007. I guess I should just be happy that I am not using any of them.
- qwerty (look at your keyboard. and I wonder why there is not a right-hand version)
- (your first name)
Saturday, April 28, 2007
"Deception and dishonesty with data:fraud in science" by David Hand
Significance, March 2007, pages 22-25
The part of this article I like most is the part where the author discussed that, despite the idealized image of scientists in the minds of the public, scientists are just human who are under pressure to be productive and to compete in order to survive the academic world. The author also observed that scientific fraud differed from other frauds such as banking frauds in that the perpetrators didn't set out to be dishonest at the beginning. It is also true that some accusation of fraud in science is arguable, especially in the gray area of "trimming" unreliable data.