Data table header descriptions |
ID_REF |
Number |
X_LOCATION |
X-coordinate of spot |
Y_LOCATION |
Y-coordinate of spot |
CH1_MEAN |
Cy5 (635nm) mean of signals |
CH1_BKD_MEAN |
Cy5 (635nm) mean of background |
CH1_SD |
Cy5 (635nm) standard deviation of signals |
CH1_BKD_SD |
Cy5 (635nm) standard deviation |
CH1_MEDIAN |
Cy5 (635nm) median of signals |
CH1_BKD_MEDIAN |
Cy5 (635nm) median of background |
CH1%>CH1_BKD+1SD |
Percent of Cy5 (635nm) signal pixels over one standard deviation over background levels |
CH1%>CH1_BKD+2SD |
Percent of Cy5 (635nm) signal pixels over two standard deviation over background levels |
CH1%_SAT |
Percent of saturated Cy5 (635nm) signal pixels |
CH1_MEDIAN_BKGR_CORR |
median pixel intensity Cy5 (635nm) minus median background of the spot |
CH1_SIGNAL_NOISE |
Cy5(635nm) signal/noise ratio |
CH1_INTENSITY |
total Cy5 (632nm) intensity of all pixels of the spot |
CH2_MEAN |
Cy3 (532nm) mean of signals |
CH2_BKD_MEAN |
Cy3 (532nm) mean of background |
CH2_SD |
Cy3 (532nm) standard deviation of signals |
CH2_BKD_SD |
Cy3 (532nm) standard deviation |
CH2%>CH2_BKD+1SD |
Percent of Cy3 (532nm) signal pixels over one standard deviation over background levels |
CH2%>CH2_BKD+2SD |
Percent of Cy3 (532nm) signal pixels over two standard deviation over background levels |
CH2%_SAT |
Percent of saturated Cy3 (532nm) signal pixels |
CH2_MEDIAN |
Cy3 (532nm) median of signals |
CH2_BKD_MEDIAN |
Cy3 (532nm) median of background |
CH2_MEDIAN_BKGR_CORR |
median pixel intensity Cy3 (532nm) minus median background of the spot |
CH2_SIGNAL_NOISE |
Cy3 (532nm) signal/noise ratio |
CH2_INTENSITY |
total Cy3 (532nm) intensity of all pixels of the spot |
DIAMETER |
Spot diameter |
MEDIANS_CH1/CH2 |
Cy5/Cy3 background corrected ratio of median intensity value of the whole feature |
MEANS_CH1/CH2 |
Cy5/Cy3 background corrected ratio of mean intensity value of the whole feature |
MEDIAN_OF_RATIOS_CH1/CH2 |
median of the Cy5/Cy3 background corrected ratios of each pixel of the feature |
MEAN_OF_RATIOS_CH1/CH2 |
mean of the Cy5/Cy3 background corrected ratios of each pixel of the feature |
RATIOS_SD_CH1/CH2 |
standard deviation of the Cy5/Cy3 background corrected ratios of each pixel of the feature |
REGRESSION_RATIO_CH1/CH2 |
slope of the least squares best-fit regression line in a scatter plot of Cy5/Cy3 for each pixel |
REGRESSION_RSQUARE_CH1/CH2 |
Square of correlation coefficient of the least-squares regression fit, proportion of regression pixels that can be described by the regression fit |
NUMBER_OF_PIXELS |
Number of pixels in the spot |
NUMBER_OF_BKD_PIXELS |
number of pixels that comprise the background for the spot |
SUM_OF_MEDIANS |
sum of background subtracted median pixel intensities of both wavelengths |
SUM_OF_MEANS |
sum of background subtracted mean pixel intensities of both wavelengths |
LOG_RATIO_CH1/CH2 |
log2 of means_ch1/ch2 |
CH1_MEAN_BKGR_CORR |
mean pixel intensity Cy5 (635nm) minus median background of the spot |
CH2_MEAN_BKGR_CORR |
mean pixel intensity Cy3 (532nm) minus median background of the spot |
CH1%_OF_TOTAL |
Channel 1 (Cy5 = 635nm) % of total |
CH2%_OF_TOTAL |
Channel 2 (Cy3 = 532nm) % of total |
PRE-VALUE |
Cy5 [635nm] % of total / Cy3 [532nm] % of total |
VALUE |
log of Cy5 [635nm] % of total / Cy3 [532nm] % of total |
FLAGS |
Feature quality assessment |