Blog Archives

My 15 practical tips for a bioinformatician

February 16, 2016
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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 y...

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Calculate the odd of winning Powerball in R

January 12, 2016
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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...

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My note on multiple testing

December 4, 2015
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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...

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How to correctly set color in the image() function?

May 15, 2015
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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,...

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Tips and Tools you may need for working on BIG data

May 8, 2015
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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...

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X11 connection error in Mac

March 11, 2015
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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...

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reshape: from long to wide format

February 26, 2015
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reshape: from long to wide format

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 ...

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How to draw venn pie-agram (multi-layer pie chart) in R?

September 25, 2014
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How to draw venn pie-agram (multi-layer pie chart) in R?

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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reshape2: convert table from wide to long format

July 15, 2014
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I found this elegant note about reshape2 from Sean Anderson's blog:http://seananderson.ca/2013/10/19/reshape.htmlBasically,reshape2 is based around two key functions: melt and cast:melt takes wide-format data and melts it into long-format data.cast tak...

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Access Google Spreadsheet directly in bash and in R

January 31, 2014
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Google Doc is a good way to share/manage documents between you and your colleagues, but sometime you want to directly access the data in terminal (e.g. bash) or in program (e.g. R), without downloading the data first. For example, I have a Google Spre...

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