P-GSE45940-1 - P-GSE45940-1

Type
normalization data transformation protocol
Description
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)
Links
Experiment E-GEOD-45940