Column definitions

Name: unique identification name of the gene

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SUID Stanford University identification

Spot Flag: spots are flagged if the PCR did not work (no band or a doublet), or if there was something abnormal about the hybridization.

CH1I: channel 1 intensity (Red probe)

CH1B: channel 1 background

CH1D: channel 1 difference

CH2I

CH2B

CH2D

CH2IN: data for channel 2 normalized to channel 1

CH2B

CH2D

CH1AB

CH2AB

SPIX: number of pixels in the spot

BGPIX: number of pixels around the spot used to calculate the background

RAT1: red/green

RAT2: green/red

RAT1N: red/normalized green

RAT2N

MRAT

REGR: Each spot is made of many pixels, and the red/green ratio is measured for every pixel. The data is graphed as a scatter plot with red signal along the Y axis and green signal along the X axis for every pixel. Ideally, every pixel would have the same color (r/g ratio) so that all of the pixels will line up along a straight line. The slope of the line indicates the r/g ratio. The regression ratio is a best fit line through all of the pixels in the red/green scatter plot.

CORR: regression correlation is a measure of how well the points on the scatter plot fits into a straight line. Numbers close to 1 mean good agreement between the individual pixels, numbers close to 0 means a wide variation in the color of each pixel.

LFRAT

CH1GTB1

CH2GTB1

CH1GTB2

CH2GTB2

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