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Sample GSM874743 Query DataSets for GSM874743
Status Public on Dec 20, 2012
Title OV3376_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 OV3376
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 52 years
tumor histology: serous
grade of tumor: 2
event (alive=1, dead=2): 2
progression (no progression=1, progression=2): 2
overall survival (os, n=months): 29.08
progression-free survival (pfs, n=months): 14.54
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/2003-09/44827.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
1 383 528 138 191 245 337 394 495 143 204 256 304 0 0 150 168 42 97 93 96 90 81 582 560 .727 1.376 1.188 1.378 1.711 1.965 32 136 1.626 .63 60 1290 8490 50 56 34 40 0 696 252 444 1.812 652 401 .552 1.565 .858 .646
2 414 611 168 271 246 340 436 623 168 282 268 352 0 0 193 254 43 105 76 73 67 61 586 620 .724 1.382 1.313 1.504 1.287 2.65 52 272 1.523 .82 80 1450 8480 48 56 49 57 -50 805 357 448 1.821 821 464 .549 1.731 .865 .791
3 656 684 151 229 505 455 678 729 154 241 527 500 0 0 341 324 41 97 94 78 82 73 960 1027 1.11 .901 .949 1.004 .94 2.028 52 254 .928 .87 80 1590 8480 48 56 63 71 -50 901 302 599 1.187 960 659 .842 1.25 .247 .322
4 228 293 125 161 103 132 204 244 129 171 79 83 0 0 96 178 30 62 65 53 57 36 235 162 .78 1.282 1.051 1.388 1.201 3.369 52 247 2.218 .63 80 1740 8480 48 56 78 86 -50 386 212 174 1.689 321 109 .592 1.384 .756 .469
5 1071 964 137 162 934 802 1077 956 147 175 940 794 0 0 240 159 61 69 100 100 100 100 1736 1734 1.165 .859 .845 .876 .884 1.32 32 213 .859 .86 70 1870 8490 49 56 91 98 0 1270 213 1057 1.131 1260 1046 .884 1.113 .178 .154
6 401 570 132 177 269 393 351 561 139 184 219 384 0 0 178 185 34 70 93 100 87 96 662 603 .684 1.461 1.753 1.774 1.316 2.733 32 176 1.574 .67 60 2020 8480 49 55 107 113 0 751 233 518 1.925 739 506 .52 2.31 .945 1.208
7 636 787 128 166 508 621 584 802 139 184 456 636 0 0 173 255 61 94 100 96 100 93 1129 1092 .818 1.222 1.395 1.135 1.395 1.924 32 160 1.452 .79 60 2180 8460 47 53 123 129 0 1037 219 818 1.611 1057 838 .621 1.838 .688 .878
8 859 1001 134 158 725 843 916 959 149 172 782 801 0 0 266 416 92 78 100 100 93 100 1568 1583 .86 1.163 1.024 1.179 1.047 1.579 32 213 1.244 .84 70 2320 8490 49 56 136 143 0 1319 208 1111 1.532 1264 1055 .653 1.35 .615 .432
9 511 524 134 160 377 364 517 466 138 172 383 306 0 0 141 218 36 67 100 93 100 93 741 689 1.036 .966 .799 .885 .912 1.826 32 172 1.129 .81 60 2460 8490 50 56 151 157 0 690 211 480 1.272 614 403 .786 1.053 .347 .074
10 629 652 131 170 498 482 616 664 135 178 485 494 0 0 108 126 35 72 100 100 100 100 980 979 1.033 .968 1.019 .955 .982 1.283 32 205 1.039 .88 70 2610 8490 49 56 165 172 0 859 224 635 1.275 875 651 .784 1.342 .351 .424
11 512 487 132 160 380 327 545 487 136 166 413 327 0 0 112 116 38 60 100 100 96 100 707 740 1.162 .861 .792 .855 .812 1.693 32 219 .879 .72 70 2750 8490 49 56 179 186 0 642 211 431 1.134 642 431 .882 1.043 .181 .061
12 358 337 135 190 223 147 353 278 146 207 218 88 0 0 198 197 49 100 67 46 63 32 370 306 1.517 .659 .404 .867 .805 3.443 52 299 1.074 .69 80 2900 8470 47 55 194 202 -50 444 250 194 .869 366 116 1.151 .532 -.203 -.911
13 353 468 147 211 206 257 348 443 156 224 201 232 0 0 75 172 46 95 100 90 96 68 463 433 .802 1.248 1.154 1.201 1.331 1.744 32 171 1.784 .73 60 3040 8480 49 55 209 215 0 617 278 339 1.644 584 306 .608 1.521 .717 .605
14 638 726 146 210 492 516 657 732 151 225 511 522 0 0 131 183 42 90 100 100 100 93 1008 1033 .953 1.049 1.022 1.009 1.062 1.309 32 221 1.117 .87 70 3200 8470 47 54 224 231 0 957 277 680 1.382 964 688 .724 1.346 .467 .429
15 402 550 130 183 272 367 401 562 136 187 271 379 0 0 64 136 38 64 100 100 100 100 639 650 .741 1.349 1.399 1.295 1.295 1.501 32 209 1.533 .79 70 3340 8490 49 56 238 245 0 725 241 484 1.778 740 499 .563 1.843 .83 .882
16 2767 1959 134 160 2633 1799 3171 2175 145 167 3037 2015 0 0 1497 917 57 59 100 100 98 100 4432 5052 1.464 .683 .663 .79 .675 1.744 52 291 .651 .96 80 3480 8490 49 57 252 260 0 2581 211 2370 .9 2866 2655 1.111 .874 -.152 -.194
17 573 667 133 157 440 510 587 648 138 172 454 491 0 0 127 222 33 66 100 96 100 96 950 945 .863 1.159 1.081 1.102 1.06 1.642 32 176 1.297 .81 60 3630 8480 49 55 268 274 0 879 207 672 1.527 854 647 .655 1.425 .611 .511
18 575 898 123 156 452 742 598 903 127 166 475 747 0 0 133 265 27 67 100 100 100 100 1194 1222 .609 1.642 1.573 1.584 1.738 1.457 32 176 1.808 .89 60 3780 8480 49 55 283 289 0 1183 206 978 2.163 1190 984 .462 2.072 1.113 1.051
19 1473 1775 126 156 1347 1619 1420 1735 126 164 1294 1579 0 0 330 429 28 58 100 100 100 100 2966 2873 .832 1.202 1.22 1.196 1.209 1.324 32 172 1.259 .91 60 3920 8480 49 55 297 303 0 2339 206 2133 1.584 2286 2080 .631 1.608 .663 .685
20 760 761 127 163 633 598 764 764 128 165 637 601 0 0 241 247 29 56 100 100 100 96 1231 1238 1.059 .945 .943 .935 .978 1.488 32 176 .957 .89 60 4070 8480 49 55 312 318 0 1003 215 788 1.245 1007 792 .803 1.243 .316 .314

Total number of rows: 41568

Table truncated, full table size 9220 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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