Publications by Xianjun Dong
X11 connection error in Mac
Typically, I log into my remote server/cluster via “ssh -X” and from there launch R program for plotting. But it always shows an error as unable to open connection to X11 display ”after a while, when you want to call functions such as plot(). This is very annoying. So that I have to exit the server and re-login again. Does thi...
1072 sym
Tips and Tools you may need for working on BIG data
Nowadays everyone is talking about big data. As a genomic scientist, I could feel hungry of a collection of tools more specialized for the mediate-to-big data we deal everyday.Here are some tips I found useful when getting, processing or visualizing large data set:1. How to download data faster than wget?We can use wget to download th...
3031 sym
How to correctly set color in the image() function?
Sometimes we want to make our own heatmap using image() function. I recently found it’s tricky to set the color option there, as its manual has very little information on col:cola list of colors such as that generated by rainbow, heat.colors, topo.colors, terrain.colors or similar functions.I posted my question on BioStars. The...
1960 sym 1 tbl
My note on multiple testing
It’s not a shame to put a note on something (probably) everyone knows and you thought you know but actually you are not 100% sure. Multiple testing is such a piece in my knowledge map.Some terms first:– Type I error (false positive) and Type II error (false negative): When we do a hypothesis test, we can categorize the result int...
5380 sym R (62 sym/2 pcs) 2 tbl
My note on multiple testing
It’s not a shame to put a note on something (probably) everyone knows and you thought you know but actually you are not 100% sure. Multiple testing is such a piece in my knowledge map.Some terms first:– Type I error (false positive) and Type II error (false negative): When we do a hypothesis test, we can categorize the result int...
5381 sym R (62 sym/2 pcs) 2 tbl
Calculate the odd of winning Powerball in R
This Wednesday’s Powerball grand prize already climbed up to $1.5 BILLION. If you choose to cash out, it would be $930 million. And it keeps increasing… So, what’s the odd of winning the jackpot prize? Here is the game rule according to Powerball.com: …we draw five white balls out of a drum with 69 balls and one red ball out of a drum ...
1738 sym R (624 sym/3 pcs) 2 img
Calculate the odd of winning Powerball in R
This Wednesday’s Powerball grand prize already climbed up to $1.5 BILLION. If you choose to cash out, it would be $930 million. And it keeps increasing…So, what’s the odd of winning the jackpot prize?Here is the game rule according to Powerball.com:…we draw five white balls out of a drum with 69 balls and one red ball out of a...
1714 sym R (616 sym/3 pcs) 2 img
My 15 practical tips for a bioinformatician
Tips below are based on the lessons I learnt from making mistakes during my years of research. It’s purely personal opinion. Order doesn’t mean anything. If you think I should include something else, please comment below.Always set a seed number when you run tools with random option, e.g. bedtools shuffle, random etc.; You (or your boss in a ...
3500 sym 2 img
My 15 practical tips for a bioinformatician
Tips below are based on the lessons I learnt from making mistakes during my years of research. It’s purely personal opinion. Order doesn’t mean anything. If you think I should include something else, please comment below.Always set a seed number when you run tools with random option, e.g. bedtools shuffle, random etc.; You (or your boss in a ...
3470 sym 2 img
Best way to draw heatmap for publication
Here are two tips I can share if you were also working on a big dataset towards a high quality heatmap:1. Don’t generate PDF using pheatmap() or heatmap.2() as (i) the file is unnecessarily SUPER large if you have a lot of data points in the heatmap, so that you can kill your Illustrator; (ii) annoying grey boxes added to the grip (...
1227 sym R (41 sym/1 pcs)