NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM874762 Query DataSets for GSM874762
Status Public on Dec 20, 2012
Title OV2842_CGH
Sample type genomic
 
Channel 1
Source name universal reference
Organism Homo sapiens
Characteristics reference: universal reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name OV2842
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 39 years
tumor histology: serous
grade of tumor: 3
event (alive=1, dead=2): 2
progression (no progression=1, progression=2): 2
overall survival (os, n=months): 15.07
progression-free survival (pfs, n=months): 10.36
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4000B
Description Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44826.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 Feb 13, 2012
Last update date Dec 20, 2012
Contact name Aslaug Helland
E-mail(s) [email protected]
Phone +47-22934431
Organization name Institute for Cancer Research, Oslo University
Department Dept of Genetics
Street address Hospital Radiumhospitalet
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platform ID GPL3523
Series (1)
GSE35783 CGH-arrays ovarian 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
1 528 738 216 234 312 504 498 729 220 250 282 495 0 0 258 432 58 119 76 76 69 61 816 777 .619 1.615 1.755 1.519 1.51 2.335 52 279 1.812 .83 80 1460 8040 56 64 34 42 -50 615 195 420 1.346 608 413 .743 1.463 .429 .549
2 1796 1319 223 223 1573 1096 714 1030 789 479 491 807 0 0 5521 1534 4919 3101 3 1 3 1 2669 1298 1.435 .697 1.644 1.662 1.729 2.169 52 279 .8 .91 80 1610 8040 56 64 49 57 -100 1099 186 913 .581 858 673 1.722 1.37 -.784 .454
3 1267 1521 217 247 1050 1274 1281 1565 533 298 1064 1318 0 0 389 624 3394 426 0 87 0 71 2324 2382 .824 1.213 1.239 1.114 1.14 1.442 32 170 1.267 .92 60 1750 8040 57 63 64 70 0 1268 206 1062 1.011 1304 1098 .989 1.032 .016 .046
4 388 428 200 245 188 183 305 405 214 267 105 160 0 0 222 271 105 212 50 38 32 19 371 265 1.027 .973 1.524 1.439 1.215 3.419 52 288 1.456 .6 80 1900 8030 55 63 78 86 -50 357 204 153 .811 338 133 1.233 1.27 -.302 .345
5 1477 1560 189 251 1288 1309 1438 1575 207 270 1249 1324 0 0 420 424 94 141 100 100 100 100 2597 2573 .984 1.016 1.06 1.008 1.021 1.281 32 219 1.025 .94 70 2050 8040 56 63 93 100 0 1300 209 1091 .847 1313 1103 1.181 .884 -.239 -.179
6 417 541 193 239 224 302 415 502 197 261 222 263 0 0 186 319 57 140 73 67 67 48 526 485 .742 1.348 1.185 1.404 1.404 2.095 52 291 1.889 .72 80 2190 8030 55 63 107 115 -50 451 199 252 1.124 418 219 .89 .987 .168 -.018
7 730 1109 195 244 535 865 718 1125 208 261 523 881 0 0 173 389 95 149 100 100 100 100 1400 1404 .618 1.617 1.685 1.536 1.589 1.596 32 215 1.686 .84 70 2340 8020 54 61 122 129 0 924 203 721 1.348 938 734 .742 1.404 .43 .49
8 997 1240 204 242 793 998 1080 1149 238 271 876 907 0 0 255 471 135 172 100 96 96 93 1791 1783 .795 1.259 1.035 1.158 1.239 1.616 32 155 1.406 .86 60 2490 8020 55 61 138 144 0 1033 202 832 1.049 958 756 .953 .863 .069 -.213
9 429 582 190 232 239 350 417 564 202 255 227 332 0 0 215 301 76 136 65 69 59 55 589 559 .683 1.464 1.463 1.715 1.497 2.088 52 298 1.748 .74 80 2630 8030 55 63 151 159 -50 485 193 292 1.221 470 277 .819 1.219 .288 .286
10 888 1063 197 241 691 822 868 1058 205 259 671 817 0 0 190 289 48 109 100 100 100 96 1513 1488 .841 1.19 1.218 1.154 1.164 1.512 32 160 1.201 .86 60 2780 8040 57 63 167 173 0 886 201 685 .991 882 681 1.009 1.015 -.012 .021
11 459 592 196 238 263 354 470 590 203 253 274 352 0 0 182 250 60 119 82 80 71 57 617 626 .743 1.346 1.285 1.249 1.284 2.809 52 264 1.587 .66 80 2920 8030 55 63 180 188 -50 493 198 295 1.122 492 293 .891 1.071 .166 .099
12 416 399 197 233 219 166 368 360 204 253 171 127 0 0 222 254 69 132 69 48 53 26 385 298 1.319 .758 .743 .646 .837 3.943 52 267 1.334 .6 80 3070 8030 55 63 195 203 -50 333 194 138 .632 300 106 1.583 .619 -.663 -.692
13 324 492 200 263 124 229 293 413 207 273 93 150 0 0 129 299 59 138 61 53 44 30 353 243 .541 1.847 1.613 2.121 1.846 3.218 52 273 3.344 .56 80 3210 8030 55 63 209 217 -50 410 219 191 1.539 344 125 .65 1.344 .622 .427
14 590 1057 204 271 386 786 564 982 206 287 360 711 0 0 134 309 52 131 100 100 96 100 1172 1071 .491 2.036 1.975 2.029 1.938 1.57 32 215 2.346 .8 70 3380 8030 55 62 226 233 0 881 226 655 1.697 818 593 .589 1.646 .763 .719
15 440 681 192 257 248 424 455 683 201 278 263 426 0 0 94 222 61 138 100 87 90 78 672 689 .585 1.71 1.62 1.691 1.61 1.853 32 224 2.897 .62 70 3520 8040 56 63 240 247 0 568 214 353 1.425 569 355 .702 1.35 .511 .433
16 3222 3227 209 268 3013 2959 3421 3374 222 286 3212 3106 0 0 858 821 75 129 100 100 100 100 5972 6318 1.018 .982 .967 .997 .944 1.252 32 170 .954 .94 60 3660 8030 56 62 255 261 0 2690 223 2466 .819 2812 2589 1.222 .806 -.289 -.311
17 489 652 187 236 302 416 528 515 193 254 341 279 0 0 229 404 56 117 76 75 69 55 718 620 .726 1.377 .818 1.46 1.381 2.634 52 296 1.777 .79 80 3800 8030 55 63 268 276 -50 543 197 347 1.148 429 233 .871 .682 .199 -.552
18 619 1101 170 244 449 857 661 1175 174 253 491 931 0 0 166 383 48 120 100 93 100 90 1306 1422 .524 1.909 1.896 1.791 1.943 1.835 32 176 2.224 .86 60 3950 8030 56 62 284 290 0 918 203 714 1.591 979 776 .629 1.58 .67 .66
19 1350 1742 192 255 1158 1487 1441 1830 191 261 1249 1575 0 0 480 637 50 126 100 96 96 96 2645 2824 .779 1.284 1.261 1.353 1.281 1.592 32 176 1.325 .89 60 4090 8030 56 62 298 304 0 1452 213 1239 1.07 1525 1313 .934 1.051 .098 .072
20 777 943 177 233 600 710 781 855 186 256 604 622 0 0 265 353 56 130 100 100 100 93 1310 1226 .845 1.183 1.03 1.19 1.054 1.674 32 170 1.29 .86 60 4240 8030 56 62 313 319 0 786 194 592 .986 713 518 1.014 .858 -.02 -.22

Total number of rows: 41568

Table truncated, full table size 9356 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap