Spatial Defects in 5896 HG-U133A GeneChips

W. B. Langdon
Mathematical and Biological Sciences
Essex University

Presented at CAMDA-2007


Introduction


Example Laser output

Next


Example GeneChip Flaw visible in Laser Scanner output

back

Example flaw in CEL file


Example large area flaw in CEL file

First CEL file in GSM2394

Quantile normalised log scaled Red suspiciously bright

Detecting Spatial Flaws


Detecting Spatial Flaws


Mean 5896 E-TABM-185

Yellow is highest

Example E-TABM-185 HG-U133A

Choose as example HG-U133A with average number of flaws.

Quantile Normalised

Yellow is highest

Example HC-U133A v average

Yellow is highest

Flaws in example E-TABM-185

Blue below average
Red above average.
Controls suppressed

Defects Matter

Blue less than half expected. Min=1/6
Red more than 2 fold more than expected. Max 17 times average.
Controls suppressed

Distribution of suspect probes in 5896 E-TABM-185

Yellow is highest
Controls suppressed

GEO/E-TABM-185 defect rate


Summary


END


Mean 5896 E-TABM-185

Yellow is highest


W.Langdon 17 Dec 2007