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, s...
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 y...
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...
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 into...
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,...
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 la...
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 asunable 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 this sound...
This is to continue on the topic of using the melt/cast functions in reshape to convert between long and wide format of data frame. Here is the example I found helpful in generating covariate table required for PEER (or Matrix_eQTL) analysis:Here ...
I was wondering how to draw a venn diagram like pie chart in R, to show the distribution of my RNA-seq reads mapped onto different annotation regions (e.g. intergenic, intron, exons etc.). A google search returns several options, including the nice one from Xiaopeng's bam2x (see below). However, he told me it's not released yet. And it's javascript...
I was wondering how to draw a venn diagram like pie chart in R, to show the distribution of my RNA-seq reads mapped onto different annotation regions (e.g. intergenic, intron, exons etc.). A google search returns several options, including the nice one...
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