Batch effects (lab effects) eg. variation due to different lab groups or processing time

http://rafalab.jhsph.edu/batch/

Batch effects are sub-groups of measurements that have qualitatively different behaviour across conditions and are unrelated to the biological or scientific variables in a study. For example, batch effects may occur if a subset of experiments was run on Monday and another set on Tuesday, if two technicians were responsible for different subsets of the experiments or if two different lots of reagents, chips or instruments were used.

http://www.nature.com/nrg/journal/v11/n10/full/nrg2825.html

Combat
http://jlab.byu.edu/ComBat/Abstract.html
Reference: Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127. [Abstract]

Confounded
An extraneous variable (for example, processing data) is said to be confounded with the outcome of interest (for example, disease state) when it correlates both with the outcome and with an independent variable of interest (for example, gene expression).