FCAN:
FlyChip anlysis pipeline
FlyChip has developed an automated microarray analysis pipeline, termed fcan, to reduce the time taken to analyse microarray expression data. This pipeline is described by the following schematic. Although the schematic suggests that this is just one script, it is in reality a collection of several programs linked together by one high level script. Key aspects of the analysis pipeline are described in greater detail in the remaining pages of this section.
Anylsis pipeline
Users are reminded that each project is divided into replica groups that correspond to each sample-control pair. Each of the replica groups is hybridised to four microarrays. Two of these hybridisations are dye swaps, meaning that the sample that was labelled with Cy3 is now labelled with Cy5 and vise versa. The analysis pipeline takes the dye swaps into account during normalisation, so that the normalised data appear to come from non-swapped experiments.
