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Sample GSM874739 Query DataSets for GSM874739
Status Public on Dec 20, 2012
Title OV3872-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 OV3872
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 48 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): 69.84
progression-free survival (pfs, n=months): 25.59
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/2003-08/43531.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) aslaug.helland@medisin.uio.no
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 GPL3522
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
1 376 592 158 235 218 357 373 598 163 239 215 363 0 0 64 135 38 64 100 100 100 96 575 578 .611 1.638 1.688 1.565 1.66 1.682 32 210 1.851 .74 70 1850 8470 75 82 49 56 0 619 246 373 1.712 625 379 .584 1.765 .775 .819
2 670 916 152 220 518 696 654 919 155 224 502 699 0 0 150 167 41 69 100 100 100 100 1214 1201 .744 1.344 1.392 1.359 1.371 1.401 32 212 1.375 .87 70 2000 8470 75 82 64 71 0 957 230 727 1.404 961 731 .712 1.455 .49 .541
3 424 557 150 221 274 336 420 544 156 224 270 323 0 0 100 123 37 71 96 100 96 96 610 593 .815 1.226 1.196 1.267 1.276 1.775 32 212 1.299 .76 70 2140 8470 75 82 78 85 0 582 231 351 1.282 569 338 .78 1.25 .358 .322
4 331 449 153 214 178 235 314 450 153 216 161 236 0 0 109 121 37 62 93 93 87 84 413 397 .757 1.32 1.466 1.274 1.367 2.712 32 220 1.431 .71 70 2290 8460 74 81 93 100 0 469 224 246 1.38 470 247 .725 1.532 .465 .615
5 849 740 146 221 703 519 894 768 152 226 748 547 0 0 206 216 37 63 100 100 100 90 1222 1295 1.355 .738 .731 .688 .748 1.665 32 226 .768 .87 70 2430 8460 74 81 107 114 0 773 231 542 .772 803 572 1.296 .764 -.374 -.388
6 402 545 144 241 258 304 397 541 149 242 253 300 0 0 120 165 39 68 100 90 93 81 562 553 .849 1.178 1.186 1.159 1.185 1.845 32 164 1.438 .82 60 2580 8470 76 82 123 129 0 570 252 318 1.232 565 314 .812 1.239 .3 .31
7 381 356 156 218 225 138 371 347 158 225 215 129 0 0 101 109 33 73 96 71 96 37 363 344 1.63 .613 .6 .549 .587 2.193 32 171 .78 .57 60 2720 8470 76 82 137 143 0 372 228 144 .641 363 135 1.56 .627 -.641 -.673
8 660 817 153 210 507 607 723 847 154 215 570 637 0 0 217 206 33 65 100 96 87 96 1114 1207 .835 1.197 1.118 1.292 1.211 2.214 32 204 1.161 .87 70 2870 8470 75 82 151 158 0 854 219 634 1.251 885 666 .799 1.168 .323 .224
9 719 745 155 215 564 530 715 743 157 221 560 528 0 0 112 142 34 68 100 100 100 100 1094 1088 1.064 .94 .943 .925 .963 1.344 52 317 .953 .89 90 3010 8460 73 82 164 173 0 779 225 554 .982 777 552 1.018 .985 -.026 -.021
10 269 303 153 199 116 104 256 303 157 205 103 104 0 0 62 79 41 68 90 61 65 26 220 207 1.115 .897 1.01 .882 1.058 2.468 52 256 1.622 .39 80 3160 8450 73 81 180 188 -50 317 208 109 .937 317 109 1.067 1.055 -.094 .078
11 673 692 153 209 520 483 661 687 157 216 508 478 0 0 101 127 39 65 100 100 100 100 1003 986 1.077 .929 .941 .913 .917 1.287 52 302 .956 .9 90 3300 8460 73 82 193 202 0 723 218 505 .971 718 500 1.03 .983 -.043 -.024
12 380 510 150 221 230 289 363 507 155 225 213 286 0 0 80 110 35 63 98 100 98 94 519 499 .796 1.257 1.343 1.269 1.254 1.774 52 254 1.396 .78 80 3450 8460 74 82 209 217 0 533 231 302 1.313 530 299 .761 1.403 .393 .489
13 456 555 150 217 306 338 450 571 155 220 300 354 0 0 83 118 37 61 100 97 100 95 644 654 .905 1.105 1.18 1.051 1.103 1.756 80 345 1.207 .82 100 3600 8460 73 83 223 233 0 580 227 353 1.154 597 370 .866 1.233 .207 .303
14 444 570 149 211 295 359 443 533 155 218 294 322 0 0 108 171 41 64 98 98 98 96 654 616 .822 1.217 1.095 1.16 1.144 1.736 80 290 1.37 .81 100 3750 8460 73 83 238 248 0 596 221 375 1.272 557 337 .786 1.145 .347 .195
15 600 921 149 220 451 701 598 903 153 227 449 683 0 0 105 190 36 68 100 100 100 100 1152 1132 .643 1.554 1.521 1.541 1.558 1.425 120 398 1.654 .9 120 3890 8460 72 84 251 263 0 963 230 733 1.625 944 714 .616 1.59 .7 .669
16 1830 1955 150 212 1680 1743 1703 1820 152 220 1553 1608 0 0 593 765 32 69 100 100 100 100 3423 3161 .964 1.038 1.035 1.019 .965 1.441 52 223 1.039 .87 90 4030 8460 73 82 266 275 0 2043 222 1822 1.084 1902 1681 .922 1.082 .117 .114
17 858 970 155 222 703 748 862 969 158 227 707 747 0 0 198 223 37 67 100 100 100 100 1451 1454 .94 1.064 1.057 1.057 1.024 1.356 120 435 1.086 .92 120 4180 8460 72 84 280 292 0 1014 232 782 1.112 1013 781 .899 1.104 .153 .143
18 192 257 155 237 37 20 175 242 160 237 20 5 0 0 66 81 39 68 38 19 15 5 57 25 1.85 .541 .25 .844 .895 4.931 52 216 4.699 .21 80 4330 8450 73 81 297 305 -50 269 248 21 .565 253 5 1.77 .261 -.824 -1.936
19 3799 3906 151 228 3648 3678 3963 3964 164 245 3812 3736 0 0 748 837 93 127 100 100 100 100 7326 7548 .992 1.008 .98 1.002 1.012 1.158 80 383 1.029 .98 110 4470 8450 71 82 309 320 0 4083 238 3844 1.054 4143 3905 .949 1.024 .076 .035
20 667 514 148 214 519 300 656 498 160 233 508 284 0 0 143 125 102 133 100 93 98 55 819 792 1.73 .578 .559 .55 .571 1.541 80 302 .622 .82 100 4620 8460 73 83 325 335 0 537 224 314 .604 521 297 1.655 .584 -.727 -.775

Total number of rows: 43104

Table truncated, full table size 9659 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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