RNA from a haploid F1 segregant from a cross between the lab strain BY4716 (isogenic to S288c) and a wild isolate strain from a California vineyard collected by R. Mortimer. The reference sample is RNA from haploid BY4716 and is the same as in Yvert et al. Nat. Genet. 2003.
Data processing
First compute l = log2(median 635 - median background 635) - log2(median 532 - median background 532). Do this for every spot on chip c. Next compute m, the mean of these l values over all spots on chip c. Now subtract m from every l value on chip c to get the final the VALUE here; if the SAMPLE has Cy5 in the name, -n is the VALUE. NULL indicates missing data due to a misshapen spot (FLAG < 0) or saturated signal.
spot number from platform GPL118 (yeast cDNA arrays manufactured by the DNA Array facility, Fred Hutchinson CRC)
CH1_MEAN
median signal at 635 nm
CH1_BKD_MEAN
median background signal at 635 nm
CH2_MEAN
median signal at 532 nm
CH2_BKD_MEAN
median background signal at 532 nm
VALUE
First compute l = log2(median 635 - median background 635) - log2(median 532 - median background 532). Do this for every spot on chip c. Next compute m, the mean of these l values over all spots on chip c. Now subtract m from every l value on chip c to get the final the VALUE here; if the SAMPLE has Cy5 in the name, -n is the VALUE. NULL indicates missing data due to a misshapen spot (FLAG < 0) or saturated signal.
FLAG
GenePix flag; 0 means okay, anything else unusable
