More notes on using LRT to test time-series data. Thanks for the discussion with Jie. swapping the levels of time factor won't change the LRT results, as if the time variable is a factor, LRT won't see it as a trajectory analysis but rather a fact... [Read more...]

In many cases, we need to perform differential expression across the time course data, e.g. finding genes that react in a condition-specific manner over time, compared to a set of baseline samples. DEseq2 has such an implementation for time-course expe... [Read more...]

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When I plotted the PCA results (e.g. scatter plot for PC1 and PC2) and was about to annotate the dataset with different covariates (e.g. gender, diagnosis, and ethic group), I noticed that it's not straightforward to annotate __2 covariates at the same time using ggplot. Here is what works ... [Read more...]

Most people know KEGG pathway, but not everyone knows that it costs at least $2000 to subscribe its database. If you want to save the cost a bit, you can manually download the KEGG pathway KGML files and install in SPIA. Here I have a workaround to dow... [Read more...]

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 ... [Read more...]

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... [Read more...]

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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... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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,... [Read more...]

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... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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... [Read more...]

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, ... [Read more...]

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... [Read more...]