SMD Schema Specifications
Column Name | Data Type | Length | Null? | Description |
REPORTER_COUNT | NUMBER | 20 | YES | |
LOG_REPORTER_COUNT | NUMBER | 20,5 | YES | |
SEQ_GENE_COUNT | NUMBER | 20 | YES | |
SEQ_COVERAGE | NUMBER | 35,25 | YES | |
LOG_SEQ_RPKM_VALUE | NUMBER | 35,25 | YES | |
PROBE_CATEGORY | NUMBER | 3 | YES | |
SEQ_RPKM_VALUE | NUMBER | 35,25 | YES | |
CH1DL_MEAN | NUMBER | 20 | YES | |
CH2DL_MEAN | NUMBER | 20 | YES | |
LOG_RAT2L_MEAN | NUMBER | 20,5 | YES | |
CH1DL_MEDIAN | NUMBER | 20 | YES | |
CH2DL_MEDIAN | NUMBER | 20 | YES | |
LOG_RAT2L_MEDIAN | NUMBER | 20,5 | YES | |
CH1DL_MEAN_ORIG | NUMBER | 20 | YES | |
CH1_TOTAL_GENE_SIGNAL | NUMBER | 35,25 | YES | Total Gene Signals |
CH1_TOTAL_GENE_SIGNAL_ERROR | NUMBER | 35,25 | YES | Errors of Total Gene Signals |
CH1_TOTAL_PROBE_SIGNAL | NUMBER | 35,25 | YES | |
CH1_TOTAL_PROBE_SIGNAL_ERROR | NUMBER | 35,25 | YES | |
CH1_TOTAL_GENE_DETECTED | NUMBER | 2 | YES | |
LOG_CH1_TOTAL_GENE_SIGNAL | NUMBER | 35,25 | YES | |
LOG_CH1_TOTAL_PROBE_SIGNAL | NUMBER | 35,25 | YES | |
LOG_CH1D_MEAN | NUMBER | 35,25 | YES | |
LOG_CH1D_MEDIAN | NUMBER | 35,25 | YES | |
EXPTID | NUMBER | 10 | NO | Link to the experiment table. |
SPOT | NUMBER | 10 | NO | Link to the spotList table |
SUID | NUMBER | 10 | NO | Link to the stanfordSeq table. |
PRINTID | NUMBER | 10 | NO | Link to the spotList table. |
DATE_MODIFIED | DATE | 7 | NO | Date record was last modified (YYYY-MM-DD). |
CH1I_MEAN | NUMBER | 20 | YES | Mean spot pixel intensity at Channel 1 (usually 532 nm). |
CH1D_MEDIAN | NUMBER | 20 | YES | Median spot pixel intensity at Channel 1 with the median-background subtracted (CH1I_MEDIAN - CH1B_MEDIAN). |
CH1I_MEDIAN | NUMBER | 20 | YES | Median spot pixel intensity at Channel 1 (usually 532 nm). |
CH1_PER_SAT | NUMBER | 20 | YES | Percentage of spot pixels at Channel 1 (usually 532 nm) that are saturated. |
CH1I_SD | NUMBER | 20 | YES | Standard deviation of the spot intensity at Channel 1 (usually 532 nm). |
CH1B_MEAN | NUMBER | 20 | YES | Mean spot background in Channel 1 (usually 532 nm). |
CH1B_MEDIAN | NUMBER | 20 | YES | Median spot background intensity in Channel 1 (usually 532 nm). |
CH1B_SD | NUMBER | 20 | YES | Standard deviation of the spot background intensity in Channel 1 (usually 532 nm). |
CH1D_MEAN | NUMBER | 20 | YES | Mean Channel 1 (usually 532 nm) intensity with the median-background subtracted (CH1I_MEAN - CH1B_MEDIAN) |
CH2I_MEAN | NUMBER | 20 | YES | Mean spot pixel intensity at Channel 2 (usually 635 nm). |
CH2D_MEAN | NUMBER | 20 | YES | Mean spot pixel intensity at Channel 2 (usually 635 nm) with the median-background subtracted (CH2I_MEAN - CH2B_MEDIAN). |
CH2D_MEDIAN | NUMBER | 20 | YES | Median spot pixel intensity at Channel 2 (usually 635 nm) with the median-background subtracted (CH2I_MEDIAN - CH2B_MEDIAN). |
CH2I_MEDIAN | NUMBER | 20 | YES | Median spot pixel intensity at Channel 2 (usually 635 nm). |
CH2_PER_SAT | NUMBER | 20 | YES | Percentage of spot pixels at Channel 2 (usually 635 nm) that are saturated. |
CH2I_SD | NUMBER | 20 | YES | Standard deviation of the spot pixel intensity at at Channel 2 (usually 635 nm). |
CH2B_MEAN | NUMBER | 20 | YES | Mean spot background intensity in Channel 2 (usually 635 nm). |
CH2B_MEDIAN | NUMBER | 20 | YES | Median spot background intensity in Channel 2 (usually 635 nm). |
CH2B_SD | NUMBER | 20 | YES | Standard deviation of the spot background intensity in Channel 2 (usually 635 nm). |
CH2BN_MEDIAN | NUMBER | 20 | YES | Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor). |
CH2DN_MEAN | NUMBER | 20 | YES | Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN). |
CH2IN_MEAN | NUMBER | 20 | YES | Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor). |
CH2DN_MEDIAN | NUMBER | 20 | YES | Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN). |
CH2IN_MEDIAN | NUMBER | 20 | YES | Normalized value of median Channel 2 (usually 635 nm) intensity (CH2_MEDIAN/Normalization factor). |
CORR | NUMBER | 20,10 | YES | Coefficient of determination for the current regression value. |
DIAMETER | NUMBER | 5 | YES | Diameter in 5m of the spot indicator. |
FLAG | NUMBER | 3 | YES | Type of flag associated with a spot. |
LOG_RAT2N_MEAN | NUMBER | 20,10 | YES | Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)]. |
LOG_RAT2N_MEDIAN | NUMBER | 20,5 | YES | Log (base 2) of the ratio of the medians of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)]. |
PIX_RAT2_MEAN | NUMBER | 20,10 | YES | Geometric mean of the pixel-by-pixel ratios of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) pixel intensities, with the median background subtracted. |
PIX_RAT2_MEDIAN | NUMBER | 20,10 | YES | Median of pixel by-pixel ratios of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) pixel intensities, with the median background subtracted. |
PERGTBCH1I_1SD | NUMBER | 3 | YES | Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 1 (usually 532 nm). |
PERGTBCH1I_2SD | NUMBER | 3 | YES | Percentage of spot pixels with intensities more than two standard deviations above the background pixel intensity, at Channel 1 (usually 532 nm). |
PERGTBCH2I_1SD | NUMBER | 3 | YES | Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 2 (usually 635 nm). |
PERGTBCH2I_2SD | NUMBER | 3 | YES | Percentage of spot pixels with intensities more than two standard deviations above the background pixel intensity, at Channel 2 (usually 635 nm). |
RAT1_MEAN | NUMBER | 20,10 | YES | Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio. |
RAT1N_MEAN | NUMBER | 20,10 | YES | Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized. |
RAT2_MEAN | NUMBER | 20,10 | YES | Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 2/Channel 1 ratio, (CH2I_MEAN - CH2B_MEDIAN)/(CH1_MEAN - CH1B_MEDIAN) or Red/Green ratio. |
RAT2_MEDIAN | NUMBER | 20,10 | YES | Ratio of the median intensities of each spot for each wavelength, with the median background subtracted. |
RAT2_SD | NUMBER | 20,10 | YES | Standard deviation of pixel intensity ratios. |
RAT2N_MEAN | NUMBER | 20,10 | YES | Channel 2/Channel 1 ratio normalized, RAT2_MEAN/Normalization factor or Red/Green mean ratio normalized. |
RAT2N_MEDIAN | NUMBER | 20,10 | YES | Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized. |
REGR | NUMBER | 20,10 | YES | Regression ratio. |
SUM_MEAN | NUMBER | 20 | YES | Sum of the arithmetic mean intensities for each wavelength, with the median background subtracted (CH1D_MEAN + CH2D_MEAN). |
SUM_MEDIAN | NUMBER | 20 | YES | Sum of the median intensities for each wavelength, with the median-background subtracted (CH1D_MEDIAN + CH2D_MEDIAN). |
TOT_BPIX | NUMBER | 6 | YES | Total number of background pixels. |
TOT_SPIX | NUMBER | 6 | YES | Total number of spot pixels. |
X_COORD | NUMBER | 6 | YES | X-coordinate in 5m of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image. |
Y_COORD | NUMBER | 6 | YES | Y-coordinate in 5m of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image. |
TOP | NUMBER | 10 | YES | Box top: int(((centerX - radius) - Xoffset) / pixelSize). |
BOT | NUMBER | 10 | YES | Box bottom: int(((centerX + radius) - Xoffset) / pixelSize). |
LEFT | NUMBER | 10 | YES | Box left: int(((centerY - radius) - yoffset) / pixelSize). |
RIGHT | NUMBER | 10 | YES | Box right: int(((centerY + radius) - yoffset) / pixelSize) |
Primary Key Name | Primary Key Column(s) |
RESULT_PK | EXPTID, SPOT |
Foreign Key Name | Foreign Key Column(s) | References |
RESULT_EXPTID_FK | EXPTID | EXPERIMENT (EXPTID) |
RESULT_PRINTID_SPOT_FK | PRINTID, SPOT | SPOTLIST (PRINTID, SPOT)) |
RESULT_SUID_FK | SUID | STANFORDSEQ (SUID) |
Index Name | Unique? | Indexed Column(s) |
RESULT_PRINTID_SPOT_FK_I | NO | PRINTID, SPOT |
RESULT_SPOT_I | NO | SPOT |
RESULT_SUID_FK_I | NO | SUID |
Constraint Name | Constraint Column | Type | Description |
RESULT_DATE_MODIFIED_NN | DATE_MODIFIED | NULL | "DATE_MODIFIED" IS NOT NULL |
RESULT_EXPTID_NN | EXPTID | NULL | "EXPTID" IS NOT NULL |
RESULT_PRINTID_NN | PRINTID | NULL | "PRINTID" IS NOT NULL |
RESULT_SPOT_NN | SPOT | NULL | "SPOT" IS NOT NULL |
RESULT_SUID_NN | SUID | NULL | "SUID" IS NOT NULL |
https://genome.unc.edu/cgi-bin/SMD/tableSpecifications?table=RESULT