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Spots or areas of the array with obvious blemishes were manually flagged and excluded from subsequent analysis.
In such cases, the original records from individual databases may have to be manually flagged and excluded entirely from the retrieved PPI set.
Aberrant and empty spots were manually flagged and excluded from further analysis.
Bad spots and regions with high unspecific binding of dye were manually flagged and excluded from the analysis.
Spots and regions with high unspecific binding of dye or dust particles were manually flagged and excluded from the analysis.
Microarray images were analyzed using ImaGene (BioDiscovery Inc ., bad spots were manually flagged, and the extracted data were used for further analysis.
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Spot data were extracted from images and manually flagged to remove artefacts before fusion.
For each array, spots that had been manually flagged due to poor hybridization and spots in which the estimated fluorescence intensity was below or equal to the estimated background signal intensity in either channel were removed before further analysis.
Using BRB-ArrayTools v3.4.0 software [ 81], manually flagged bad spots were eliminated and the local background was subtracted before averaging the replicate features on the array.
Manually flagged bad spots were eliminated and the local background was subtracted prior to averaging of replicate features on the array.
The new array data presented here as well as the previous Stanford arrays were quality controlled to manually flag and exclude apparent problematic spots.
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