About Sébastien

Enjoys turning raw (big, noisy and convoluted!) biological data into knowledge… using any tools that informatics has to offer!

Is a p-value needed?

Much has been written on the need for statistics in genome-scale molecular biology.  Very clever analytical approaches were devised, taking the form of carefully crafted and freely downloadable software packages.  But still, every month or so, I meet with students and researchers facing a similar dilemma:  they need to decide whether to report the strength of an effect (eg. gene X is over-expressed by 4.5-fold in condition A vs. B) or the significance of such effect (eg. gene X is overexpressed [...]

By | 2016-11-08T09:30:17+00:00 September 12, 2014|Categories: Statistics|2 Comments

Assessing enrichment

Working on a set of RNA-seq of AML patient samples, I stumble on gene X.  When its expression is high, 50% of the samples are mutated on gene Y, a mutation that has a prevalence of only 20% in the rest of the dataset.  Is there a link between these two observations?  Let's put some numbers on this:  among the 131 samples of the dataset, 28 show mutations on gene Y, 6 have high expression of X and 3 have both "features".  The table below is [...]

By | 2016-11-08T09:30:18+00:00 May 21, 2014|Categories: Uncategorized|0 Comments