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Sample GSM874776 Query DataSets for GSM874776
Status Public on Dec 20, 2012
Title OV4641-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 OV4641
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 65 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): 39.08
progression-free survival (pfs, n=months): 22.07
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/2003-08/43532.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
1 287 418 147 239 140 179 291 410 148 241 144 171 0 0 48 91 35 56 93 100 90 71 319 315 .782 1.279 1.188 1.234 1.214 1.987 32 201 .851 .56 70 1780 8930 57 64 42 49 0 503 288 215 1.539 493 206 .65 1.429 .622 .515
2 567 793 135 242 432 551 557 829 138 245 422 587 0 0 107 180 32 52 100 100 100 100 983 1009 .784 1.275 1.391 1.236 1.293 1.517 32 212 1.459 .84 70 1940 8920 56 63 58 65 0 954 291 663 1.535 998 706 .651 1.674 .618 .743
3 337 418 141 234 196 184 337 406 143 241 196 172 0 0 99 112 34 45 93 90 93 75 380 368 1.065 .939 .878 1.035 .958 2.222 32 170 1.09 .63 60 2080 8920 57 63 73 79 0 503 282 221 1.13 489 207 .885 1.056 .176 .079
4 308 393 137 229 171 164 305 375 138 236 168 146 0 0 59 78 33 49 100 93 100 81 335 314 1.043 .959 .869 .941 .961 1.671 32 171 1.063 .73 60 2230 8920 57 63 88 94 0 473 276 197 1.154 451 176 .866 1.046 .207 .065
5 677 750 137 240 540 510 694 787 138 240 557 547 0 0 142 160 33 46 100 100 100 100 1050 1104 1.059 .944 .982 .912 .979 1.536 32 220 1.005 .87 70 2380 8920 56 63 102 109 0 903 289 614 1.137 947 658 .88 1.182 .185 .241
6 397 698 135 228 262 470 397 703 137 230 262 475 0 0 79 126 29 45 100 100 100 100 732 737 .557 1.794 1.813 1.822 1.801 1.422 32 164 1.842 .89 60 2520 8920 57 63 117 123 0 840 274 566 2.159 846 572 .463 2.182 1.11 1.126
7 332 317 135 232 197 85 295 296 137 231 160 64 0 0 73 77 29 41 100 66 100 33 282 224 2.318 .431 .4 .326 .266 2.713 12 104 .494 .49 50 2660 8920 57 62 131 136 0 382 279 102 .519 356 77 1.926 .481 -.945 -1.055
8 525 850 136 242 389 608 557 842 138 242 421 600 0 0 122 135 31 49 100 100 96 100 997 1021 .64 1.563 1.425 1.641 1.471 1.458 32 159 1.568 .84 60 2810 8920 57 63 146 152 0 1023 291 732 1.881 1013 722 .532 1.715 .912 .778
9 643 571 138 235 505 336 642 583 140 235 504 348 0 0 97 99 34 52 100 100 100 100 841 852 1.503 .665 .69 .646 .663 1.496 52 309 .696 .83 90 2950 8910 54 63 158 167 0 687 283 404 .801 702 419 1.249 .831 -.321 -.267
10 274 321 134 227 140 94 272 323 137 230 138 96 0 0 63 76 32 45 94 69 94 51 234 234 1.489 .671 .696 .61 .662 3.006 52 224 .716 .46 80 3100 8920 56 64 174 182 0 386 273 113 .808 389 116 1.237 .837 -.307 -.256
11 644 574 137 233 507 341 646 584 142 236 509 351 0 0 115 130 34 46 100 100 100 94 848 860 1.487 .673 .69 .622 .69 1.637 52 302 .733 .86 90 3240 8910 54 63 187 196 0 691 280 410 .809 703 422 1.235 .83 -.305 -.269
12 384 548 137 231 247 317 387 550 141 240 250 319 0 0 74 91 34 51 100 100 98 100 564 569 .779 1.283 1.276 1.293 1.247 1.49 52 300 1.304 .83 90 3390 8920 55 64 202 211 0 660 278 382 1.545 662 384 .647 1.536 .627 .619
13 443 539 136 224 307 315 453 543 138 230 317 319 0 0 122 96 34 49 96 100 95 96 622 636 .975 1.026 1.006 1.054 1.02 1.706 80 341 .973 .81 100 3540 8920 55 65 217 227 0 649 270 379 1.235 654 384 .81 1.211 .304 .276
14 450 496 134 227 316 269 444 484 137 229 310 257 0 0 98 94 32 51 100 100 100 98 585 567 1.175 .851 .829 .843 .817 1.526 52 250 .873 .8 90 3680 8910 54 63 231 240 0 597 273 324 1.025 583 309 .976 .998 .035 -.003
15 471 635 136 226 335 409 473 651 138 228 337 425 0 0 82 141 31 52 100 96 100 95 744 762 .819 1.221 1.261 1.175 1.254 1.733 120 513 1.329 .85 130 3830 8910 52 65 244 257 0 764 272 492 1.469 784 512 .681 1.518 .555 .602
16 1891 1500 133 227 1758 1273 1857 1413 134 227 1724 1186 0 0 465 590 30 54 100 100 100 98 3031 2910 1.381 .724 .688 .656 .698 1.621 52 250 .778 .87 90 3970 8910 54 63 260 269 0 1805 273 1532 .872 1701 1427 1.147 .828 -.198 -.272
17 940 1013 137 227 803 786 964 1050 137 230 827 823 0 0 248 279 31 53 100 98 100 96 1589 1650 1.022 .979 .995 .965 .97 1.462 120 437 1.014 .93 120 4120 8910 53 65 274 286 0 1219 273 946 1.178 1264 991 .849 1.198 .236 .26
18 161 254 134 220 27 34 153 259 134 225 19 39 0 0 48 53 31 50 40 38 15 11 61 58 .794 1.259 2.053 1.15 1.5 4.448 52 191 4.806 .12 80 4260 8900 54 62 290 298 -50 306 265 41 1.516 312 47 .66 2.47 .6 1.305
19 3458 3492 132 223 3326 3269 3796 4036 135 227 3664 3813 0 0 1308 1395 34 46 100 99 100 97 6595 7477 1.017 .983 1.041 .94 .99 1.733 120 435 .999 .96 120 4410 8910 53 65 303 315 0 4203 268 3934 1.183 4858 4589 .845 1.252 .242 .325
20 688 750 134 214 554 536 685 760 135 216 551 546 0 0 97 134 34 47 100 100 100 100 1090 1097 1.034 .968 .991 .949 .986 1.367 80 304 1.053 .88 100 4560 8910 54 64 319 329 0 903 258 645 1.164 915 657 .859 1.193 .22 .254

Total number of rows: 43104

Table truncated, full table size 9627 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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