MDS - miRNA expression guppy brain
Miles W.
03/25/21
Data initialization
Data input, cleaning, wrangling
sample size = 27 Fish
Data type
miRNA expression, ie counts of mature reads mapped to precursors, is ratio data, a count of zero indicates no expression
from: What is the difference between ordinal, interval and ratio variables? Why should I care?
https://www.graphpad.com/support/faq/what-is-the-difference-between-ordinal-interval-and-ratio-variables-why-should-i-care/
In the 1940s, Stanley Smith Stevens introduced four scales of measurement: nominal, ordinal, interval, and ratio. These are still widely used today as a way to describe the characteristics of a variable. Knowing the scale of measurement for a variable is an important aspect in choosing the right statistical analysis.
Data Types - four scales of measurement
A ratio variable, has all the properties of an interval variable, and also has a clear definition of 0.0. When the variable equals 0.0, there is none of that variable. Examples of ratio variables include enzyme activity, dose amount, reaction rate, flow rate, concentration, pulse, weight, length, temperature in Kelvin (0.0 Kelvin really does mean “no heat”), survival time.
Extract mature read counts
Currently only using mature read counts which account for majority of total counts.
Back to using all reads, ie. mature + star + loop counts - 03/31/21
Mirdeep Normalization Method:
Q2 - How are miRNA expression values reported by the qunatification module normalized?
A - Expression values are normalized by library size and multiplied by a factor of 1E6 which corresponds technically to counts per million mapped miRNA reads (RPM). The library size is the total number of reads mapping to miRNA precursors.
Mature read count distribution
Justification for metric or non-metric approach
REASONS TO USE PARAMETRIC TESTS Reason 1: Parametric tests can perform well with skewed and nonnormal distributions
MDS - 2D plots
