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Sample GSM90273 Query DataSets for GSM90273
Status Public on Dec 31, 2005
Title AT2_Latent
Sample type RNA
 
Channel 1
Source name Latent
Organism Homo sapiens
Characteristics Latent
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ref
Organism Homo sapiens
Characteristics Ref
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: HUVEC, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27494.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 30, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3284
Series (1)
GSE3956 Antiangiogenic Antithrombin

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN 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.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN 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.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN 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)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 2463 1392 507 195 1956 1197 2515 1452 514 199 2008 1257 0 0 439 298 90 50 100 100 100 100 3153 3265 1.634 .612 .626 .608 .628 1.256 52 312 .588 .9 90 2120 7880 75 84 43 52 0 3164 443 2720 1.391 3300 2857 .719 1.423 .476 .509
2 10870 7341 495 199 10375 7142 11805 7954 513 200 11310 7755 0 0 3588 2937 91 47 100 100 100 100 17517 19065 1.453 .688 .686 .596 .709 1.87 80 365 .7 .96 100 2260 7880 75 85 57 67 0 16684 452 16232 1.565 18077 17625 .639 1.558 .646 .64
3 15299 12966 494 193 14805 12773 15522 13505 501 197 15028 13312 0 0 2668 3869 83 43 100 100 100 100 27578 28340 1.159 .863 .886 .786 .91 1.724 52 312 .909 .94 90 2410 7880 75 84 72 81 0 29468 439 29030 1.961 30693 30255 .51 2.013 .971 1.009
4 3066 2887 493 198 2573 2689 3242 2895 503 207 2749 2697 0 0 623 659 93 59 100 100 100 100 5262 5446 .957 1.045 .981 1.051 1.051 1.24 52 326 1.029 .96 90 2560 7890 76 85 87 96 0 6561 450 6111 2.375 6580 6130 .421 2.23 1.248 1.157
5 36761 8447 502 206 36259 8241 39646 9279 512 214 39144 9073 0 0 15320 4336 97 61 100 98 98 97 44500 48217 4.4 .227 .232 .195 .232 2.032 80 354 .229 .94 100 2710 7880 75 85 102 112 0 19198 468 18730 .517 21089 20620 1.936 .527 -.953 -.925
6 2790 1645 517 212 2273 1433 2845 1515 521 215 2328 1303 0 0 984 622 88 46 100 100 100 100 3706 3631 1.586 .63 .56 .646 .597 1.573 80 325 .603 .93 100 2850 7890 76 86 116 126 0 3739 482 3257 1.433 3443 2961 .698 1.272 .519 .347
7 18781 10312 524 216 18257 10096 19439 9860 526 221 18915 9644 0 0 3994 2121 79 74 100 100 100 100 28353 28559 1.808 .553 .51 .556 .533 1.248 52 289 .535 .94 90 2990 7880 75 84 130 139 0 23436 491 22945 1.257 22409 21918 .796 1.159 .33 .213
8 7836 2311 531 217 7305 2094 8555 2326 536 222 8024 2109 0 0 2325 970 80 70 100 96 100 96 9399 10133 3.489 .287 .263 .245 .27 1.895 80 378 .292 .94 100 3140 7880 75 85 145 155 0 5252 493 4759 .651 5286 4793 1.535 .597 -.618 -.743
9 2471 2130 525 212 1946 1918 2786 2235 526 216 2261 2023 0 0 990 955 89 49 96 98 94 96 3864 4284 1.015 .986 .895 .963 .949 1.622 52 301 .983 .93 90 3290 7880 75 84 160 169 0 4841 482 4359 2.24 5080 4598 .446 2.033 1.164 1.024
10 2984 2449 513 209 2471 2240 3229 2663 516 215 2716 2454 0 0 1119 875 86 52 95 100 93 100 4711 5170 1.103 .907 .904 .978 .875 2.006 80 362 .856 .92 100 3440 7890 76 86 175 185 0 5566 475 5091 2.06 6052 5577 .485 2.053 1.043 1.038
11 5248 8131 511 213 4737 7918 5568 9237 515 217 5057 9024 0 0 1318 3114 89 56 100 100 100 100 12655 14081 .598 1.672 1.784 1.548 1.773 1.458 80 342 1.823 .95 100 3590 7880 75 85 190 200 0 18480 484 17995 3.799 20993 20509 .263 4.056 1.926 2.02
12 16189 8971 526 213 15663 8758 16573 8808 524 216 16047 8595 0 0 5998 3335 86 48 100 100 100 100 24421 24642 1.788 .559 .536 .563 .571 1.34 52 289 .545 .93 90 3720 7880 75 84 203 212 0 20389 484 19905 1.271 20018 19534 .787 1.217 .346 .284
13 9380 3137 537 214 8843 2923 9474 3031 540 221 8937 2817 0 0 2742 896 80 50 100 100 100 100 11766 11754 3.025 .331 .315 .33 .312 1.306 52 314 .315 .88 90 3870 7880 75 84 218 227 0 7130 486 6643 .751 6889 6402 1.331 .716 -.413 -.481
14 2324 1315 519 212 1805 1103 2379 1224 537 224 1860 1012 0 0 746 522 222 93 100 100 98 100 2908 2872 1.636 .611 .544 .613 .578 1.549 52 325 .597 .91 90 4020 7880 75 84 233 242 0 2989 482 2507 1.389 2782 2300 .72 1.237 .474 .306
15 2994 2070 526 220 2468 1850 3071 2180 542 248 2545 1960 0 0 933 510 229 177 98 100 92 98 4318 4505 1.334 .75 .77 .77 .78 1.613 52 306 .691 .88 90 4170 7870 74 83 248 257 0 4705 500 4205 1.704 4955 4455 .587 1.75 .769 .808
16 24059 6899 531 221 23528 6678 26966 7550 539 233 26435 7329 0 0 10277 2850 111 114 100 100 100 100 30206 33764 3.523 .284 .277 .291 .29 1.805 80 391 .267 .93 100 4320 7880 75 85 263 273 0 15680 502 15177 .645 17159 16657 1.55 .63 -.632 -.666
17 19224 6628 520 219 18704 6409 21044 6992 526 224 20524 6773 0 0 7941 2504 82 52 100 100 100 100 25113 27297 2.918 .343 .33 .348 .345 1.396 52 289 .329 .95 90 4470 7880 75 84 278 287 0 15064 498 14566 .779 15891 15393 1.284 .75 -.361 -.415
18 2706 1825 509 216 2197 1609 2910 1852 521 221 2401 1636 0 0 1100 693 110 61 100 98 98 98 3806 4037 1.365 .732 .681 .79 .751 1.726 52 236 .696 .93 80 4610 7880 76 84 293 301 0 4148 491 3657 1.664 4209 3718 .601 1.549 .735 .631
19 21500 10599 522 212 20978 10387 24034 12136 540 232 23512 11924 0 0 7305 3897 246 191 100 100 100 100 31365 35436 2.02 .495 .507 .489 .509 1.573 80 435 .49 .95 110 4760 7880 74 85 306 317 0 24089 482 23607 1.125 27582 27100 .889 1.153 .17 .205
20 14981 7451 536 225 14445 7226 18769 7661 564 250 18233 7436 0 0 6707 2942 129 94 100 100 100 100 21671 25669 1.999 .5 .408 .538 .501 1.698 52 246 .471 .95 80 4910 7880 76 84 323 331 0 16934 511 16423 1.137 17411 16900 .88 .927 .185 -.11

Total number of rows: 43008

Table truncated, full table size 9811 Kbytes.




Supplementary data files not provided
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