P-GSE45940-1 - P-GSE45940-1

normalization data transformation protocol
The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock. ID_REF = ID number VALUE = Normalized log2 ratio median intensity of Ch1(Cy5)/Ch2(Cy3) (Ch2=reference)
Experiment E-GEOD-45940