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Sample GSM874788 Query DataSets for GSM874788
Status Public on Dec 20, 2012
Title OV3546_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 OV3546
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 40 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): 21.12
progression-free survival (pfs, n=months): 3.49
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/2003-09/44831.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 GPL3528
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
1 650 405 507 342 143 63 639 375 623 394 132 33 0 0 164 228 1626 513 0 1 0 0 206 165 2.27 .441 .25 1.361 1.366 3.888 52 291 .041 .03 80 1950 4960 36 44 31 39 -50 450 380 70 .49 417 37 2.042 .278 -1.03 -1.847
2 754 382 568 359 186 23 726 351 596 367 158 -8 0 0 185 195 198 186 42 17 17 7 209 150 8.087 .124 null .805 1.123 3.031 52 267 .223 .05 80 2100 4960 36 44 46 54 -50 425 399 26 .137 390 -9 7.274 null -2.863 null
3 734 394 601 345 133 49 696 342 603 352 95 -3 0 0 169 283 136 172 36 25 21 11 182 92 2.714 .368 null 1.333 1.155 5.788 52 274 5.463 .15 80 2240 4960 36 44 60 68 -50 438 384 54 .41 380 -3 2.441 null -1.288 null
4 637 398 558 321 79 77 609 384 565 341 51 63 0 0 121 204 100 181 34 26 23 9 156 114 1.026 .975 1.235 1.539 1.453 3.812 52 268 10.286 .13 80 2390 4960 36 44 75 83 -50 442 357 86 1.084 427 70 .923 1.373 .116 .458
5 844 691 495 319 349 372 860 670 505 343 365 351 0 0 251 370 114 188 71 68 65 46 721 716 .938 1.066 .962 1.451 1.222 2.914 32 164 1.734 .56 60 2530 4960 37 43 90 96 0 768 355 414 1.185 745 390 .844 1.069 .245 .096
6 510 395 397 326 113 69 498 345 404 342 101 19 0 0 156 249 109 190 44 21 21 11 182 120 1.638 .611 .188 .965 1.218 4.66 52 288 6.507 .11 80 2680 4960 36 44 104 112 -50 439 362 77 .679 384 21 1.473 .209 -.559 -2.257
7 467 450 364 302 103 148 449 451 368 328 85 149 0 0 120 206 86 184 50 42 30 23 251 234 .696 1.437 1.753 1.248 1.324 3.776 52 259 6.4 .19 80 2830 4960 36 44 119 127 -50 500 336 165 1.598 501 166 .626 1.949 .676 .963
8 439 470 340 314 99 156 425 450 356 334 85 136 0 0 146 241 102 183 48 44 28 19 255 221 .635 1.576 1.6 1.548 1.327 3.353 52 259 7.215 .18 80 2970 4960 36 44 133 141 -50 523 349 173 1.752 500 151 .571 1.779 .809 .831
9 936 941 263 364 673 577 952 915 281 379 689 551 0 0 173 367 136 175 100 84 100 75 1250 1240 1.166 .857 .8 .704 .8 2.478 32 155 1.107 .67 60 3110 4950 36 42 148 154 0 1046 405 641 .953 1017 613 1.049 .889 -.069 -.17
10 327 420 253 351 74 69 314 385 260 368 61 34 0 0 98 225 76 183 40 30 21 13 143 95 1.072 .932 .557 1.988 2 2.347 52 288 7.409 .28 80 3270 4960 36 44 163 171 -50 467 390 77 1.037 428 38 .965 .62 .052 -.69
11 877 1189 274 295 603 894 857 1200 268 325 583 905 0 0 124 288 60 200 100 100 100 100 1497 1488 .674 1.483 1.552 1.435 1.466 1.442 32 148 1.721 .82 60 3400 4950 36 42 177 183 0 1322 328 994 1.648 1334 1006 .607 1.726 .721 .787
12 812 844 273 316 539 528 787 866 312 339 514 550 0 0 138 257 143 194 100 91 100 83 1067 1064 1.021 .98 1.07 1.054 1.05 1.315 12 90 1.442 .65 50 3540 4940 35 40 191 196 0 938 351 587 1.089 963 611 .918 1.19 .123 .251
13 546 876 275 285 271 591 515 917 274 306 240 632 0 0 130 359 61 173 100 91 83 66 862 872 .459 2.181 2.633 1.889 2.531 3.566 12 98 4.023 .52 50 3690 4950 36 41 206 211 0 974 317 657 2.425 1019 703 .412 2.928 1.278 1.55
14 575 832 277 286 298 546 616 772 281 337 339 486 0 0 119 296 59 194 100 100 91 66 844 825 .546 1.832 1.434 1.793 2.041 2.014 12 98 2.725 .67 50 3830 4950 36 41 220 225 0 925 318 607 2.037 858 540 .491 1.594 1.026 .673
15 648 1093 305 281 343 812 667 1059 306 319 362 778 0 0 157 460 82 172 93 93 81 87 1155 1140 .422 2.367 2.149 2.236 2.163 2.145 32 160 2.855 .77 60 3990 4950 36 42 236 242 0 1215 312 903 2.632 1177 865 .38 2.389 1.396 1.257
16 1839 2277 294 340 1545 1937 1914 2448 414 467 1620 2108 0 0 520 776 955 1100 87 84 21 43 3482 3728 .798 1.254 1.301 1.272 1.351 1.466 32 160 1.331 .92 60 4130 4950 36 42 250 256 0 2532 378 2154 1.394 2722 2344 .717 1.447 .479 .533
17 670 1156 275 336 395 820 635 1138 282 355 360 802 0 0 271 496 68 180 94 90 86 80 1215 1162 .482 2.076 2.228 2.184 2.38 2.284 52 267 2.694 .7 80 4290 4940 34 42 265 273 0 1285 374 912 2.308 1265 892 .433 2.477 1.207 1.308
18 282 434 277 337 5 97 266 425 283 351 -11 88 0 0 73 208 68 200 15 26 3 7 102 77 .052 19.4 null 1.937 2.246 3.453 52 278 51.867 .05 80 4430 4960 36 44 279 287 -50 483 375 108 21.568 473 98 .046 null 4.431 null
19 2006 2318 398 350 1608 1968 2074 2383 415 353 1676 2033 0 0 670 814 130 173 96 96 96 93 3576 3709 .817 1.224 1.213 1.151 1.26 1.957 32 148 1.264 .87 60 4590 4950 36 42 296 302 0 2577 389 2188 1.361 2649 2260 .735 1.349 .444 .431
20 994 983 473 370 521 613 966 921 490 387 493 551 0 0 197 406 133 188 100 88 93 72 1134 1044 .85 1.177 1.118 1.024 1.097 2.149 80 486 1.583 .71 110 4730 4940 32 43 307 318 0 1093 411 682 1.308 1024 613 .764 1.243 .387 .313

Total number of rows: 43104

Table truncated, full table size 9483 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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