NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM72072 Query DataSets for GSM72072
Status Public on Aug 27, 2005
Title ovca9-Gr2
Sample type RNA
 
Channel 1
Source name UHR
Organism Homo sapiens
Characteristics UHR
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name ovca9-Gr2 Total RNA
Organism Homo sapiens
Characteristics ovca9-Gr2 Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31942.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 Aug 26, 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 GPL2790
Series (1)
GSE3208 Distinction between serous tumors of low malignant potential and serous carcinomas

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
1 954 1175 211 310 743 865 995 1179 214 347 784 869 0 0 251 373 32 217 100 94 100 88 1608 1653 .859 1.164 1.108 1 1 1 52 268 1 .85 80 2070 7940 78 86 43 51 0 1351 356 994 1.338 1355 999 .747 1.274 .42 .349
2 1052 1218 212 321 840 897 1102 1226 244 357 890 905 0 0 299 339 162 233 100 96 94 92 1737 1795 .936 1.068 1.017 1 1 1 52 263 1 .82 90 2210 7940 77 86 56 65 0 1400 369 1031 1.227 1409 1040 .815 1.169 .296 .225
3 3260 1037 212 304 3048 733 3315 1065 278 329 3103 761 0 0 997 361 229 163 100 93 100 85 3781 3864 4.158 .24 .245 1 1 1 120 560 1 .71 130 2360 7940 75 88 69 82 0 1192 349 843 .276 1224 875 3.618 .282 -1.855 -1.827
4 8370 1689 217 298 8153 1391 9786 1701 260 329 9569 1403 0 0 4285 752 179 151 100 100 100 92 9544 10972 5.861 .171 .147 1 1 1 52 290 1 .92 90 2500 7940 77 86 85 94 0 1941 343 1599 .196 1955 1613 5.099 .169 -2.35 -2.569
5 1270 925 221 289 1049 636 1241 832 235 328 1020 543 0 0 512 421 62 162 100 90 100 81 1685 1563 1.649 .606 .532 1 1 1 32 197 1 .81 70 2660 7930 77 84 102 109 0 1063 332 731 .697 956 624 1.435 .612 -.521 -.709
6 624 994 221 329 403 665 600 1000 228 361 379 671 0 0 212 307 64 168 100 94 98 84 1068 1050 .606 1.65 1.77 1 1 1 52 248 1 .72 80 2800 7950 79 87 116 124 0 1143 378 764 1.897 1149 771 .527 2.035 .923 1.025
7 523 1710 208 307 315 1403 521 1708 215 325 313 1401 0 0 91 365 54 145 100 100 100 100 1718 1714 .225 4.454 4.476 1 1 1 52 313 1 .85 90 2930 7940 77 86 128 137 0 1966 353 1613 5.12 1963 1610 .195 5.145 2.356 2.363
8 7152 3367 198 319 6954 3048 7185 3438 200 342 6987 3119 0 0 1678 746 34 178 100 100 100 100 10002 10106 2.281 .438 .446 1 1 1 52 276 1 .93 80 3080 7940 78 86 144 152 0 3870 367 3503 .504 3952 3585 1.985 .513 -.989 -.963
9 1934 1019 176 307 1758 712 1925 994 181 334 1749 687 0 0 529 348 43 232 100 96 100 67 2470 2436 2.469 .405 .393 1 1 1 52 275 1 .72 80 3230 7950 79 87 159 167 0 1171 353 818 .466 1143 790 2.148 .451 -1.103 -1.147
10 475 492 165 292 310 200 496 490 171 297 331 198 0 0 100 152 43 133 100 59 100 28 510 529 1.55 .645 .598 1 1 1 32 153 1 .52 60 3380 7940 79 85 175 181 0 566 336 230 .742 563 228 1.349 .688 -.431 -.54
11 748 393 175 271 573 122 206 371 178 311 31 100 0 0 1461 221 32 251 48 23 32 3 695 131 4.697 .213 3.226 1 1 1 52 269 1 .3 80 3510 7940 78 86 187 195 -100 452 311 140 .245 426 115 4.086 3.708 -2.031 1.891
12 1984 686 195 318 1789 368 2030 637 200 361 1835 319 0 0 471 242 39 287 100 55 100 23 2157 2154 4.861 .206 .174 1 1 1 52 298 1 .27 90 3670 7950 78 87 202 211 0 789 366 423 .236 732 367 4.229 .2 -2.08 -2.323
13 1255 741 214 317 1041 424 1332 758 231 363 1118 441 0 0 405 284 90 235 94 69 94 48 1465 1559 2.455 .407 .394 1 1 1 52 242 1 .7 80 3800 7940 78 86 216 224 0 852 364 487 .468 871 507 2.136 .453 -1.095 -1.141
14 716 648 243 336 473 312 674 487 275 351 431 151 0 0 231 707 114 157 100 50 100 25 785 582 1.516 .66 .35 1 1 1 32 160 1 .59 60 3960 7960 81 87 233 239 -100 745 386 359 .758 560 174 1.319 .403 -.399 -1.312
15 6187 1554 224 349 5963 1205 6535 1378 492 1212 6311 1029 0 0 1079 1018 2992 5957 100 1 69 0 7168 7340 4.949 .202 .163 1 1 1 52 342 1 .56 90 4100 7940 77 86 245 254 0 1786 401 1385 .232 1584 1183 4.305 .187 -2.106 -2.416
16 2291 1130 188 294 2103 836 2333 1119 197 323 2145 825 0 0 543 244 63 172 100 100 100 98 2939 2970 2.516 .398 .385 1 1 1 52 313 1 .89 90 4250 7950 78 87 260 269 0 1299 338 961 .457 1286 948 2.189 .442 -1.13 -1.178
17 640 545 182 279 458 266 630 505 189 308 448 226 0 0 136 166 59 177 100 69 100 25 724 674 1.722 .581 .504 1 1 1 52 264 1 .5 80 4390 7940 78 86 275 283 0 626 321 306 .668 580 260 1.498 .58 -.583 -.786
18 439 478 182 270 257 208 433 429 191 297 251 159 0 0 72 164 56 164 100 50 98 21 465 410 1.236 .809 .633 1 1 1 52 258 1 .47 80 4540 7950 79 87 290 298 0 549 310 239 .93 493 183 1.075 .728 -.104 -.458
19 2489 601 183 288 2306 313 2749 557 225 347 2566 269 0 0 796 231 165 602 99 10 99 0 2619 2835 7.367 .136 .105 1 1 1 120 497 1 .13 120 4690 7940 76 88 303 315 0 691 331 360 .156 640 309 6.41 .12 -2.68 -3.053
20 1958 764 183 289 1775 475 2045 769 206 312 1862 480 0 0 453 195 119 168 100 92 100 75 2250 2342 3.737 .268 .258 1 1 1 52 274 1 .73 90 4830 7950 78 87 318 327 0 878 332 546 .308 884 552 3.251 .296 -1.701 -1.755

Total number of rows: 43008

Table truncated, full table size 9079 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap