Identification and normalization of plate effects in cDNA microarray data
Centre for Mathematical Sciences
Lund Institute of Technology,
Introducing a new way of visualizing cDNA microarray data we have identified
a new type of systematic variation, which we refer to as plate effects. We
believe that plate effects are due to non-biological differences in the cDNA
clones products spotted onto the microarray slides. By comparing the consistency
of all replicates (both within and between slides) after performing 42 different
normalization strategies we claim that the plate effects arenon-negligible
and should be corrected for in addition to the already known intensity dependent
effects. For comparison between normalization strategies we introduce a novel
robust genewise variability measure, which we call measure of reproducibility.
In our case, we also found that not doing background correction improves
the reproducibility significantly.
cDNA microarrays; systematic variation; artifacts; plate effects; normalization