SPT Column Header Explanations

image row – the zero based row index of the gene on the image.

image column – the zero based column index of the gene on the image.

plate #

plate row

plate column

1 int – the Cy3 intensity

1 back – the Cy3 background

1 int-back – the Cy3 intensity minus the background (i.e. the Cy3 signal)

2 int – the Cy5 intensity

2 back – the Cy5 background

2 int-back – the Cy5 intensity minus the background (i.e. the Cy3 signal)

spot x – the x-axis value for the center of the pixel of the spot

spot y – the y-axis value for the center of the pixel of the spot

1 sd oneloc – the standard deviation of the Cy3 background intensity from the corner of the spot area that has the lowest median background. This is an estimate of the Cy3 noise around the spot.

1 sd corners – the standard deviation of the Cy3 background intensity from all corners around the spot, an estimate of the uniformity of the Cy3 noise around the spot.

2 sd oneloc – the standard deviation of the Cy5 background intensity from the corner of the spot area that has the lowest median background. This is an estimate of the Cy5 noise around the spot.

2 sd corners – the standard deviation of the Cy5 background intensity from all corners around the spot, an estimate of the uniformity of the Cy5 noise around the spot.

1.1,2.1,ratio.1 – the Cy3, Cy5 and ratio of the Cy3/Cy5 intensity in the first quadrant of the spot.

1.2,2.2,ratio.2 – the Cy3, Cy5 and ratio of the Cy3/Cy5 intensity in the second quadrant of the spot.

1.3,2.3,ratio.3 – the Cy3, Cy5 and ratio of the Cy3/Cy5 intensity in the third quadrant of the spot.

1.4,2.4,ratio.4 – the Cy3, Cy5 and ratio of the Cy3/Cy5 intensity in the fourth quadrant of the spot.

ratio – the ratio of Cy3/Cy5 for the entire spot.

ratio error – the standard deviation of the quadrant ratios divided by the mean of the quadrant ratios.