inst/app/md/home.md

In wpm: Well Plate Maker

Welcome to Well Plate Maker!

WPM is a shiny application (web-based UI) allowing you to create a map of well-plate for your experiments by controlling batch effects.

Indeed, the placement of samples on a plate can raise questions when we want to take into account batch effects (because a placement on a plate is a technical source of variation), which may confound the discovery of real biological variation. The question therefore arises mainly when the samples are divided into different groups (here, we speak of a group to define a category of the factor to be studied. Eg: different treatments to compare, different stages of development, etc.)

WPM is a software tool to simplify the randomization of different sample groups (biological conditions to be compared, treatments, blocking factors, etc.) while accounting for many practical constraints (buffer solution and control samples, location effects, number and type of plates, etc.).

The plate map is built using a backtracking-inspired algorithm with some specific spatial constraints which can be chosen by the user. The plate is filled randomly (and not linearly), i.e. the plate is not filled from left to right (or from top to bottom, etc.). This avoids having to end up with a checkerboard plate map when the numbers in the groups are unbalanced (which would correspond to a form of batch effect).

There are 3 other tabs:

• The Parameters tab where to prepare your data for wpm.
• The Results tab where you will see your results.
• The Help tab where you will find a tutorial explaining how to use WPM.

wpm documentation built on Nov. 8, 2020, 5:34 p.m.