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Sample GSM874819 Query DataSets for GSM874819
Status Public on Dec 20, 2012
Title OV3581_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 OV3581
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 66 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): 134.44
progression-free survival (pfs, n=months): 50.82
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/2003-08/43886.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
1 498 425 204 171 294 254 483 425 204 176 279 254 0 0 71 90 41 44 100 100 100 100 548 533 1.157 .864 .91 .833 .806 1.403 12 98 .931 .78 50 1830 6040 65 70 56 61 0 384 154 229 .781 384 229 1.281 .823 -.357 -.282
2 440 471 186 171 254 300 450 439 190 173 264 268 0 0 67 95 41 48 100 100 100 100 554 532 .847 1.181 1.015 1.164 1.232 1.445 12 98 1.286 .75 50 1980 6030 64 69 71 76 0 426 154 271 1.067 397 242 .937 .917 .094 -.125
3 194 220 174 181 20 39 168 192 185 190 -6 11 0 0 87 106 58 67 19 25 13 13 59 5 .513 1.95 null 1.635 1.938 3.418 52 314 1.471 .58 80 2130 6040 64 72 85 93 -50 199 164 35 1.762 173 10 .568 null .817 null
4 285 301 170 163 115 138 265 286 257 174 95 123 0 0 103 89 1023 60 0 78 0 50 253 218 .833 1.2 1.295 1.44 1.301 3.846 32 164 1.089 .63 60 2280 6050 66 72 101 107 0 272 147 125 1.084 258 111 .922 1.17 .117 .226
5 682 638 163 163 519 475 652 644 226 168 489 481 0 0 253 215 880 52 9 100 0 96 994 970 1.093 .915 .984 .955 .822 2.181 32 222 .028 .18 70 2420 6050 65 72 114 121 0 576 147 429 .827 582 435 1.209 .889 -.274 -.17
6 312 327 162 160 150 167 327 322 162 165 165 162 0 0 94 87 35 35 91 91 66 91 317 327 .898 1.113 .982 .992 1.148 4.59 12 104 1.03 .68 50 2570 6040 65 70 130 135 0 295 145 151 1.006 291 146 .994 .887 .008 -.173
7 226 207 162 158 64 49 192 189 163 161 30 31 0 0 98 89 39 41 44 42 30 23 113 61 1.306 .766 1.033 .815 .666 3.068 52 314 .872 .52 80 2720 6030 63 71 144 152 -50 187 143 44 .692 171 28 1.446 .934 -.532 -.099
8 405 444 156 160 249 284 380 445 165 173 224 285 0 0 73 103 47 84 100 100 100 83 533 509 .877 1.141 1.272 1.105 1.123 1.492 12 98 1.319 .84 50 2860 6030 64 69 159 164 0 401 145 257 1.03 402 257 .97 1.15 .043 .201
9 1062 1052 164 168 898 884 1063 1085 165 169 899 917 0 0 207 230 34 42 100 100 100 100 1782 1816 1.016 .984 1.02 .976 1.026 1.33 32 176 1.01 .89 60 3010 6040 65 71 174 180 0 950 152 799 .889 980 828 1.124 .922 -.169 -.118
10 427 371 164 156 263 215 416 370 171 172 252 214 0 0 63 65 47 61 100 100 100 91 478 466 1.223 .817 .849 .804 .772 1.608 12 90 .863 .72 50 3150 6020 63 68 188 193 0 335 141 194 .739 334 193 1.354 .767 -.437 -.382
11 1008 897 175 167 833 730 980 914 176 172 805 747 0 0 140 134 39 45 100 100 100 100 1563 1552 1.141 .876 .928 .872 .874 1.232 32 232 .888 .92 70 3300 6040 64 71 202 209 0 810 151 660 .792 826 675 1.263 .838 -.337 -.254
12 794 944 173 159 621 785 847 958 177 169 674 799 0 0 132 105 42 48 100 100 100 100 1406 1473 .791 1.264 1.185 1.283 1.168 1.311 12 98 1.343 .9 50 3440 6030 64 69 217 222 0 853 144 709 1.142 866 722 .876 1.071 .192 .099
13 557 626 167 162 390 464 564 626 173 177 397 464 0 0 107 157 44 79 100 100 100 91 854 861 .841 1.19 1.169 1.16 1.215 1.473 12 90 1.091 .87 50 3580 6020 63 68 231 236 0 566 146 419 1.075 566 419 .93 1.056 .104 .079
14 593 683 168 169 425 514 599 655 174 178 431 486 0 0 70 89 33 47 100 100 100 100 939 917 .827 1.209 1.128 1.209 1.158 1.251 12 98 1.247 .91 50 3730 6030 64 69 246 251 0 617 153 464 1.093 592 439 .915 1.019 .128 .027
15 848 1324 171 171 677 1153 883 1323 174 174 712 1152 0 0 276 438 42 51 100 100 100 100 1830 1864 .587 1.703 1.618 1.742 1.774 1.38 32 220 1.724 .95 70 3890 6040 64 71 261 268 0 1196 154 1042 1.539 1195 1041 .65 1.462 .622 .548
16 2143 2453 170 170 1973 2283 2195 2532 174 172 2025 2362 0 0 582 731 39 43 100 100 100 100 4256 4387 .864 1.157 1.166 1.134 1.195 1.297 32 170 1.197 .96 60 4030 6030 64 70 276 282 0 2216 154 2063 1.045 2288 2134 .957 1.054 .064 .076
17 1119 1229 174 174 945 1055 1115 1301 175 182 941 1127 0 0 406 399 41 47 100 100 100 100 2000 2068 .896 1.116 1.198 1.121 1.169 1.307 52 266 1.121 .94 80 4180 6030 63 71 290 298 0 1110 157 953 1.009 1175 1018 .991 1.082 .012 .114
18 197 194 172 161 25 33 194 187 173 166 22 26 0 0 63 70 36 41 28 32 9 13 58 48 .758 1.32 1.182 1.247 1.239 3.651 52 277 1.31 .42 80 4320 6030 63 71 304 312 -50 175 145 30 1.193 169 23 .839 1.068 .254 .095
19 2262 2760 177 170 2085 2590 2249 2632 177 176 2072 2462 0 0 1078 1383 36 49 100 100 100 100 4675 4534 .805 1.242 1.188 1.179 1.174 1.594 32 164 1.262 .94 60 4470 6040 65 71 320 326 0 2494 154 2340 1.122 2378 2224 .891 1.074 .166 .102
20 1421 1580 187 179 1234 1401 1445 1564 195 191 1258 1385 0 0 315 281 65 83 100 100 100 100 2635 2643 .881 1.135 1.101 1.163 1.117 1.334 80 505 1.115 .96 110 4620 6040 62 73 332 343 0 1427 162 1266 1.026 1413 1251 .975 .995 .037 -.008

Total number of rows: 43104

Table truncated, full table size 9819 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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