NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM874824 Query DataSets for GSM874824
Status Public on Dec 20, 2012
Title OV4070_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 OV4070
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 72 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): 111.97
progression-free survival (pfs, n=months): 65.82
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4000A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44489.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
1 296 276 133 181 163 95 280 268 137 191 147 87 0 0 132 120 35 67 78 55 67 34 258 234 1.716 .583 .592 .748 .734 3.037 52 278 .883 .58 80 1490 8040 40 48 37 45 -50 311 204 107 .657 302 98 1.523 .667 -.606 -.584
2 309 263 126 178 183 85 333 254 129 186 207 76 0 0 113 90 33 72 86 51 80 23 268 283 2.153 .464 .367 .459 .505 3.111 52 295 .613 .43 80 1640 8040 40 48 52 60 -50 296 201 96 .523 286 86 1.91 .414 -.934 -1.273
3 449 406 123 162 326 244 444 385 129 172 321 223 0 0 155 131 37 61 93 93 90 81 570 544 1.336 .748 .695 .732 .71 1.885 32 164 .802 .75 60 1790 8040 41 47 68 74 0 458 183 275 .843 434 251 1.186 .783 -.246 -.353
4 232 179 123 171 109 8 229 173 130 183 106 2 0 0 104 71 33 62 71 15 57 7 117 108 13.625 .073 .019 .383 .434 4.208 52 249 .216 .13 80 1930 8040 40 48 81 89 -50 202 193 9 .083 195 2 12.091 .021 -3.596 -5.556
5 619 764 137 187 482 577 637 762 142 194 500 575 0 0 133 212 41 72 100 100 100 96 1059 1075 .835 1.197 1.15 1.14 1.125 1.543 32 164 1.28 .83 60 2080 8040 41 47 97 103 0 861 211 650 1.349 859 648 .741 1.296 .432 .374
6 281 272 140 187 141 85 291 251 143 192 151 64 0 0 100 110 35 70 82 46 71 26 226 215 1.659 .603 .424 .549 .635 2.911 52 297 1.087 .53 80 2220 8040 40 48 110 118 -50 307 211 96 .679 283 72 1.472 .478 -.558 -1.066
7 547 721 138 171 409 550 573 737 140 180 435 566 0 0 111 186 31 61 100 100 100 100 959 1001 .744 1.345 1.301 1.314 1.394 1.454 32 176 1.461 .88 60 2370 8040 41 47 126 132 0 813 193 620 1.515 831 638 .66 1.466 .6 .552
8 456 755 128 173 328 582 458 754 137 182 330 581 0 0 118 216 41 64 100 100 93 100 910 911 .564 1.774 1.761 1.8 1.81 1.526 32 213 1.894 .88 70 2520 8050 41 48 140 147 0 851 195 656 2 850 655 .5 1.984 1 .988
9 237 346 122 166 115 180 198 282 126 171 76 116 0 0 112 206 34 61 65 63 51 48 295 192 .639 1.565 1.526 1.764 1.783 3.164 52 292 2.178 .67 80 2660 8030 39 47 154 162 -50 390 187 203 1.764 318 131 .567 1.72 .819 .782
10 700 435 127 177 573 258 739 435 131 179 612 258 0 0 146 93 35 66 100 96 100 93 831 870 2.221 .45 .422 .459 .481 1.566 32 216 .471 .74 70 2810 8040 40 47 169 176 0 490 199 291 .507 490 291 1.971 .475 -.979 -1.074
11 379 386 119 174 260 212 371 393 123 179 252 219 0 0 76 114 30 63 100 87 100 75 472 471 1.226 .815 .869 .658 .903 2.455 32 223 1.111 .72 70 2950 8040 40 47 183 190 0 435 196 239 .919 443 247 1.088 .979 -.122 -.03
12 256 315 120 165 136 150 247 281 120 175 127 116 0 0 128 153 31 64 69 65 59 44 286 243 .907 1.103 .913 1.031 1.217 2.663 52 298 1.375 .7 80 3100 8030 39 47 198 206 -50 355 186 169 1.243 317 131 .805 1.029 .314 .042
13 358 473 128 172 230 301 341 499 130 181 213 327 0 0 116 171 32 74 96 90 87 81 531 540 .764 1.309 1.535 1.212 1.323 2.665 32 172 1.525 .76 60 3250 8040 41 47 214 220 0 533 194 339 1.475 562 369 .678 1.73 .561 .791
14 677 394 132 187 545 207 699 370 134 194 567 183 0 0 125 113 34 73 100 87 100 71 752 750 2.633 .38 .323 .324 .347 1.782 32 214 .375 .66 70 3380 8040 40 47 226 233 0 444 211 233 .428 417 206 2.336 .364 -1.224 -1.459
15 370 316 131 182 239 134 367 307 132 191 236 125 0 0 77 105 35 77 100 75 96 37 373 361 1.784 .561 .53 .523 .611 2.481 32 230 .809 .47 70 3540 8030 39 46 242 249 0 356 205 151 .632 346 141 1.583 .597 -.662 -.744
16 2309 1351 126 177 2183 1174 2533 1451 130 188 2407 1274 0 0 588 403 31 74 100 100 100 100 3357 3681 1.859 .538 .529 .524 .57 1.29 32 222 .521 .94 70 3690 8040 40 47 257 264 0 1522 199 1323 .606 1635 1436 1.65 .596 -.722 -.745
17 472 566 122 167 350 399 496 550 123 175 374 383 0 0 143 195 32 63 100 100 93 90 749 757 .877 1.14 1.024 1.122 1.146 1.804 32 176 1.244 .83 60 3830 8040 41 47 272 278 0 638 188 450 1.285 620 432 .778 1.154 .361 .207
18 670 738 112 169 558 569 687 737 116 174 575 568 0 0 168 231 29 63 100 96 100 96 1127 1143 .981 1.02 .988 .888 1.067 2.221 32 172 1.114 .86 60 3980 8040 41 47 287 293 0 832 190 641 1.149 831 640 .87 1.113 .201 .155
19 769 948 117 176 652 772 810 999 120 177 693 823 0 0 288 396 33 72 96 96 93 93 1424 1516 .845 1.184 1.188 1.133 1.265 1.487 32 172 1.283 .89 60 4120 8040 41 47 301 307 0 1068 198 870 1.334 1126 927 .749 1.338 .416 .42
20 344 348 112 162 232 186 329 270 119 171 217 108 0 0 191 229 32 64 84 53 65 46 418 325 1.247 .802 .498 .792 .754 3.641 52 289 1.073 .78 80 4270 8030 39 47 315 323 -50 392 183 210 .903 304 122 1.107 .561 -.146 -.834

Total number of rows: 41568

Table truncated, full table size 9118 Kbytes.




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