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Sample GSM90102 Query DataSets for GSM90102
Status Public on Dec 30, 2005
Title PT315_2
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PT315_2
Organism Homo sapiens
Characteristics PT315_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24148.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 29, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3044
Series (1)
GSE3933 Prostate Cancer

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
1 498 352 151 62 347 290 525 338 153 64 374 276 0 0 224 156 37 18 91 100 83 97 637 650 1.197 .836 .738 .891 .756 1.906 80 380 .76 .9 100 1670 8210 80 90 74 84 0 317 56 261 .753 305 249 1.328 .665 -.409 -.589
2 354 211 147 62 207 149 371 210 152 64 224 148 0 0 140 63 34 17 83 97 80 95 356 372 1.389 .72 .661 .882 .742 2.345 80 319 .563 .85 100 1810 8210 80 90 88 98 0 190 56 134 .648 189 133 1.542 .595 -.625 -.748
3 2281 1366 152 66 2129 1300 2722 1630 184 84 2570 1564 0 0 1048 569 214 114 92 97 91 91 3429 4134 1.638 .611 .609 .662 .613 1.601 80 421 .59 .97 110 1950 8200 78 89 101 112 0 1231 59 1171 .55 1468 1409 1.818 .548 -.862 -.867
4 4369 9447 163 74 4206 9373 2970 7306 197 97 2807 7232 0 0 3856 7961 225 122 86 100 77 100 13579 10039 .449 2.228 2.576 2.924 2.306 1.95 80 377 2.164 .98 100 2110 8210 80 90 118 128 0 8511 67 8444 2.008 6582 6515 .498 2.321 1.006 1.215
5 759 1415 154 65 605 1350 745 1401 158 71 591 1336 0 0 455 930 42 32 90 100 86 98 1955 1927 .448 2.231 2.261 2.359 2.285 1.974 52 278 2.251 .94 90 2260 8200 79 88 133 142 0 1275 59 1216 2.01 1262 1204 .497 2.037 1.007 1.026
6 394 273 158 63 236 210 405 253 165 69 247 190 0 0 169 108 44 35 80 94 73 88 446 437 1.124 .89 .769 .987 .891 1.867 52 305 .743 .88 90 2390 8210 80 89 146 155 0 246 57 189 .802 228 171 1.247 .693 -.319 -.529
7 1166 601 163 65 1003 536 1333 690 182 76 1170 625 0 0 641 259 116 57 84 100 76 96 1539 1795 1.871 .534 .534 .678 .537 1.96 52 316 .471 .95 90 2530 8200 79 88 160 169 0 541 59 483 .481 622 563 2.077 .481 -1.055 -1.055
8 5285 6567 159 66 5126 6501 4207 5534 176 79 4048 5468 0 0 4226 4978 106 59 92 100 90 98 11627 9516 .788 1.268 1.351 1.657 1.29 2.511 80 401 1.234 .97 100 2690 8200 79 89 176 186 0 5916 59 5857 1.143 4986 4926 .875 1.217 .192 .283
9 1454 1284 148 61 1306 1223 1589 1318 156 66 1441 1257 0 0 882 766 41 23 86 100 86 100 2529 2698 1.068 .936 .872 1.104 .852 2.459 52 299 .9 .95 90 2830 8210 80 89 190 199 0 1157 55 1102 .844 1187 1132 1.185 .786 -.245 -.348
10 645 651 152 68 493 583 799 660 173 119 647 592 0 0 290 353 85 125 83 91 83 83 1076 1239 .846 1.183 .915 1.065 1.129 1.402 12 99 1.356 .9 50 2980 8190 80 85 207 212 0 586 61 525 1.065 595 533 .939 .824 .091 -.279
11 2398 2361 141 60 2257 2301 2738 2590 163 87 2597 2530 0 0 1206 1114 121 119 94 100 91 98 4558 5127 .981 1.019 .974 1.142 1.023 1.698 120 588 .989 .97 120 3120 8200 78 90 218 230 0 2127 54 2073 .918 2333 2279 1.089 .878 -.123 -.188
12 2005 1287 147 65 1858 1222 2318 1395 190 110 2171 1330 0 0 981 604 186 176 90 93 87 90 3080 3501 1.52 .658 .613 .716 .638 1.788 32 203 .651 .96 70 3290 8190 79 86 237 244 0 1159 59 1101 .593 1257 1198 1.688 .552 -.755 -.857
13 879 1027 144 60 735 967 928 1124 158 69 784 1064 0 0 534 597 69 49 76 100 75 94 1702 1848 .76 1.316 1.357 1.664 1.341 1.998 52 280 1.242 .96 90 3410 8210 80 89 248 257 0 925 54 871 1.185 1013 959 .844 1.223 .245 .29
14 362 362 150 64 212 298 380 379 150 67 230 315 0 0 123 121 33 23 90 100 81 96 510 545 .711 1.406 1.37 1.455 1.407 1.662 32 147 1.247 .85 60 3580 8200 81 87 267 273 0 326 58 268 1.266 341 284 .79 1.234 .341 .303
15 4282 4675 146 64 4136 4611 4367 4765 156 71 4221 4701 0 0 2984 3099 76 40 90 100 90 100 8747 8922 .897 1.115 1.114 1.394 1.117 2.229 80 420 1.07 .98 110 3700 8210 79 90 276 287 0 4212 58 4154 1.004 4293 4235 .996 1.003 .006 .005
16 1569 2529 148 65 1421 2464 1615 2660 160 76 1467 2595 0 0 988 1443 79 44 87 100 87 100 3885 4062 .577 1.734 1.769 1.949 1.65 1.649 80 458 1.638 .97 110 3850 8200 78 89 291 302 0 2278 59 2220 1.562 2396 2338 .64 1.594 .644 .672
17 328 335 157 68 171 267 341 327 160 73 184 259 0 0 135 134 38 26 78 100 75 94 438 443 .64 1.561 1.408 1.824 1.545 2.256 52 272 1.265 .84 80 4000 8200 80 88 308 316 0 302 61 241 1.407 295 233 .711 1.268 .492 .343
18 312 219 158 71 154 148 350 223 168 79 192 152 0 0 113 51 45 35 78 100 75 87 302 344 1.041 .961 .792 .885 .814 1.864 32 132 .59 .65 60 4160 8190 80 86 325 331 0 197 64 133 .866 201 137 1.155 .713 -.208 -.488
19 1250 2465 143 65 1107 2400 1339 2556 148 72 1196 2491 0 0 621 1210 38 38 95 100 94 100 3507 3687 .461 2.168 2.083 2.294 2.151 1.545 120 638 2.14 .97 130 4290 8190 76 89 334 347 0 2221 59 2162 1.953 2303 2244 .512 1.876 .966 .908
20 331 258 149 70 182 188 352 275 154 80 203 205 0 0 129 78 38 43 84 90 71 87 370 408 .968 1.033 1.01 1.101 .973 1.675 32 144 .746 .78 60 4460 8210 82 88 355 361 0 232 63 169 .931 248 185 1.075 .91 -.104 -.136

Total number of rows: 43008

Table truncated, full table size 9254 Kbytes.




Supplementary data files not provided
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