基因芯片数据字段

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