Harshlight flow diagram. For each chip, an error image is obtained by subtracting the median across all chips and analyzed for the presence of extended defects. If any is found, the chip is discarded; otherwise it is searched for compact defects. Isolated compact defects are then subtracted from the error image prior to searching for diffuse defects. The expression values within compact and diffuse defects are then purged from the chip.
Suárez-Fariñas et al. BMC Bioinformatics 2005 6:294 doi:10.1186/1471-2105-6-294