If the specks are in only one channel then this is likely due to some other type of noise that will interfere with the accuracy of the intensity reading. If either of these types of specks occurs in a spot, then the spot is flagged as bad. Donuts thus far have been flagged based on the presence of saturated pixels in the outside rim of the spot. With most of the signal occurring on the outside rim of the spot, a donut spot have a hollow middle, which lowers the intensity readings relative to what they would have been had the spot been uniformly hybridized. Finally, spots that have streaks, heavy background, or any other type of phenomenon that may lead to a miscalculation of the intensity reading are flagged bad.
Streaks vary a lot in their type.
Some are very distinguishable, and some are just dark enough to give a possible false reading. If something in the spot looks wrong, then it is wrong, and should be flagged. Please click on the following link examples of flagged spots to see some examples of the spots that were talked about above. Spots are flagged based on the Genepix image and not from the SMD image. The Examples of flagged spots page displays both the Genepix and SMD images for problematic spots, illustrating the differences between the two types of images.