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Sample GSM874800 Query DataSets for GSM874800
Status Public on Dec 20, 2012
Title OV4713_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 OV4713
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 47 years
tumor histology: serous
grade of tumor: 3
event (alive=1, dead=2): 1
progression (no progression=1, progression=2): 2
overall survival (os, n=months): 68.88
progression-free survival (pfs, n=months): 37.73
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/2003-07/43164.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 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
1 481 557 188 220 293 337 525 576 190 224 337 356 0 0 112 176 40 55 100 100 100 83 630 693 .869 1.15 1.056 1.048 1.008 1.773 12 98 1.464 .78 50 2120 8400 61 66 53 58 0 581 229 351 1.199 601 371 .834 1.102 .262 .14
2 641 1036 194 208 447 828 654 1046 194 210 460 838 0 0 210 274 41 52 100 100 90 100 1275 1298 .54 1.852 1.822 2.116 1.94 2.143 32 164 1.88 .86 60 2280 8410 62 68 69 75 0 1080 217 863 1.932 1091 874 .518 1.9 .95 .926
3 470 457 207 213 263 244 448 467 208 216 241 254 0 0 140 117 39 52 91 91 91 91 507 495 1.078 .928 1.054 .967 .991 1.45 12 104 .941 .8 50 2420 8400 61 66 83 88 0 477 222 254 .968 487 265 1.034 1.099 -.048 .136
4 371 376 194 208 177 168 390 355 196 211 196 147 0 0 102 97 40 52 87 93 81 78 345 343 1.054 .949 .75 1.118 .965 3.15 32 164 1.03 .63 60 2570 8410 62 68 98 104 0 392 217 175 .99 370 153 1.01 .782 -.015 -.355
5 868 768 190 216 678 552 913 813 198 222 723 597 0 0 352 333 45 71 100 100 91 91 1230 1320 1.228 .814 .826 .8 .85 2.13 12 104 .904 .78 50 2710 8400 61 66 112 117 0 801 225 576 .849 848 623 1.178 .861 -.236 -.216
6 479 651 200 217 279 434 506 647 201 219 306 430 0 0 136 119 45 56 100 100 83 100 713 736 .643 1.556 1.405 1.814 1.468 1.819 12 104 1.704 .77 50 2850 8400 61 66 126 131 0 679 226 453 1.622 675 448 .616 1.465 .698 .551
7 371 404 194 214 177 190 357 421 197 218 163 207 0 0 88 127 40 48 100 83 83 83 367 370 .932 1.073 1.27 1.363 1.328 1.908 12 104 1.499 .51 50 2990 8410 62 67 140 145 0 421 223 198 1.119 439 216 .893 1.324 .163 .405
8 642 749 191 192 451 557 664 740 194 199 473 548 0 0 193 193 40 54 100 100 93 100 1008 1021 .81 1.235 1.159 1.35 1.176 1.792 32 156 1.228 .86 60 3150 8410 62 68 156 162 0 781 200 581 1.288 772 571 .776 1.208 .365 .273
9 854 741 190 200 664 541 869 739 194 206 679 539 0 0 173 190 42 54 100 100 100 100 1205 1218 1.227 .815 .794 .782 .84 1.507 52 317 .856 .88 90 3300 8400 59 68 169 178 0 773 209 564 .85 771 562 1.177 .828 -.235 -.273
10 298 385 193 207 105 178 283 362 196 212 90 155 0 0 68 111 41 53 87 87 56 78 283 245 .59 1.695 1.722 1.763 1.826 2.612 32 198 2.02 .56 70 3440 8400 60 67 184 191 0 401 216 186 1.768 378 162 .566 1.796 .822 .845
11 800 633 202 209 598 424 817 653 203 214 615 444 0 0 149 124 38 53 100 100 100 100 1022 1059 1.41 .709 .722 .704 .733 1.433 52 274 .714 .88 80 3590 8400 60 68 199 207 0 660 218 442 .739 681 463 1.352 .753 -.436 -.41
12 437 445 198 213 239 232 426 433 200 216 228 220 0 0 90 104 42 58 100 96 98 90 471 448 1.03 .971 .965 .9 .962 1.832 52 254 1.044 .77 80 3740 8400 60 68 214 222 0 464 222 242 1.012 452 229 .988 1.006 .018 .009
13 588 609 188 196 400 413 587 600 193 197 399 404 0 0 121 134 44 57 100 100 98 100 813 803 .969 1.033 1.013 1.029 1.042 1.565 52 272 1.071 .85 80 3880 8400 60 68 228 236 0 635 204 431 1.077 626 421 .929 1.056 .107 .078
14 326 332 175 167 151 165 333 337 186 215 158 170 0 0 94 113 71 408 75 3 53 0 316 328 .915 1.093 1.076 1.348 1.227 2.036 32 187 3.98 .64 70 4040 8400 60 67 244 251 0 346 174 172 1.14 351 177 .878 1.122 .188 .166
15 715 854 193 204 522 650 735 858 196 208 542 654 0 0 126 162 43 68 100 100 100 100 1172 1196 .803 1.245 1.207 1.235 1.226 1.393 80 386 1.318 .9 110 4170 8400 58 69 255 266 0 891 213 678 1.299 895 682 .77 1.258 .377 .332
16 6126 5480 189 185 5937 5295 6435 5576 213 202 6246 5391 0 0 2665 2858 323 125 100 100 100 96 11232 11637 1.121 .892 .863 .78 .898 1.657 52 244 .926 .95 90 4320 8410 60 69 271 280 0 5715 193 5522 .93 5815 5622 1.075 .9 -.105 -.152
17 939 1010 181 176 758 834 959 1038 200 187 778 862 0 0 231 286 250 95 98 98 85 98 1592 1640 .909 1.1 1.108 1.086 1.086 1.644 120 413 .955 .83 120 4470 8400 58 70 285 297 0 1053 184 870 1.147 1082 899 .872 1.155 .198 .208
18 193 195 195 187 -2 8 188 190 200 197 -7 3 0 0 47 60 43 58 11 11 5 3 6 -4 null null null 1.479 1.325 2.963 52 196 2.556 .26 80 4600 8380 58 66 300 308 -50 203 195 8 null 198 3 null null null null
19 4395 4163 195 194 4200 3969 4506 4173 202 202 4311 3979 0 0 996 785 55 63 100 100 100 100 8169 8290 1.058 .945 .923 .963 .929 1.242 80 355 .918 .95 110 4750 8400 58 69 313 324 0 4341 202 4139 .985 4352 4149 1.015 .963 -.021 -.055
20 608 726 185 177 423 549 582 695 192 187 397 518 0 0 157 232 56 66 100 100 98 96 972 915 .77 1.298 1.305 1.262 1.284 1.52 80 375 1.443 .85 110 4890 8390 57 68 327 338 0 757 185 573 1.353 725 540 .739 1.361 .437 .444

Total number of rows: 43104

Table truncated, full table size 9633 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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