| Data table header descriptions |
| ID_REF |
ID in YMD – Yale Microarray Database |
| CH1_median |
Channel 1 (635 nm, Cy5, Experiment) median pixel intensity |
| CH2_median |
Channel 2 (532 nm, Cy3, Reference) median pixel intensity |
| CH1_back |
Channel 1 Background |
| CH2_back |
Channel 2 Background |
| CH1_MEAN |
Channel 1 Mean |
| CH2_MEAN |
|
| CH1_SD |
Channel 1 Standard Deviation |
| CH2_SD |
Channel 2 Standard Deviation |
| pixels |
Number of pixels used to determine signal. |
| bpixels |
Number of pixels used to determine background. |
| x |
X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
| y |
Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
| diameter |
diameter in µm of the feature-indicator |
| %>CH1_back+1SD |
percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 1 |
| %>CH1_back+2SD |
percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 1 |
| %>CH2_back+1SD |
percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 2 |
| %>CH2_back+2SD |
percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 2 |
| CH1_%Sat |
percentage of pixel saturation within feature for Channel 1 |
| CH2_%Sat |
percentage of pixel saturation within feature for Channel 2 |
| QUALITY |
Compute median for the "B635 median" and "B532 median" respectively. Store them in median_B635 and median_B532 respectively. For each row, set quality to 0 if any of following is true: a: "F635 Median - B635"/max(median_B635 ,"B635 Median")<1 and "F532 Median - B532"/max(median_B532,"B532 Median")<1; b: flag <0; c: "% > B532+1SD" <75 and "% > B635+1SD" <75. else, set the quality to 1 |
| flag |
An extension of GenePix 3.0 flags described at http://twiki.med.yale.edu/twiki/bin/view/YMD/YMDFlagFields |
| ratio_calc |
(CH1_median-CH1_back)/(CH2_median-CH2_back) |
| VALUE |
log ratio (log2 of PRE_VALUE) |
| norm_factor |
Normalization factor calculated as described at http://twiki.med.yale.edu/twiki/bin/view/YMD/NormalizationAndFilterMethods |
| PRE_VALUE |
[(Experiment channel median intensity - background)/(Reference channel median intensity - background)]*(norm_factor) |
