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Sample GSM874752 Query DataSets for GSM874752
Status Public on Dec 20, 2012
Title OV4044_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 OV4044
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): 92.14
progression-free survival (pfs, n=months): 17.66
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/2003-08/43883.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
1 402 340 151 158 251 182 389 351 154 164 238 193 0 0 76 69 37 56 100 91 100 83 433 431 1.379 .725 .811 .688 .682 1.657 12 90 .832 .66 50 1840 5580 43 48 33 38 0 335 156 179 .714 346 190 1.4 .799 -.486 -.324
2 345 368 156 151 189 217 356 347 164 160 200 196 0 0 97 112 45 47 93 100 84 93 406 396 .871 1.148 .98 1.16 1.057 2.004 32 170 1.254 .73 60 1990 5590 44 50 48 54 0 362 149 214 1.131 342 193 .884 .965 .178 -.051
3 185 182 151 159 34 23 166 159 157 162 15 0 0 0 85 76 42 53 28 30 7 15 57 15 1.478 .676 null 1.321 1.556 3.504 52 299 1.15 .3 80 2140 5600 44 52 62 70 -50 179 157 23 .666 157 0 1.501 null -.586 null
4 289 244 144 144 145 100 297 254 150 145 153 110 0 0 88 79 28 44 91 75 75 58 245 263 1.45 .69 .719 .61 .776 3.933 12 104 .782 .53 50 2280 5600 45 50 77 82 0 240 142 98 .679 250 108 1.472 .708 -.558 -.498
5 655 610 152 154 503 456 649 668 153 157 497 514 0 0 173 233 36 44 100 93 100 87 959 1011 1.103 .907 1.034 .833 .927 1.809 32 170 .996 .87 60 2430 5590 44 50 92 98 0 601 152 449 .893 658 506 1.12 1.019 -.163 .027
6 348 264 146 155 202 109 346 253 153 161 200 98 0 0 48 61 35 46 100 83 100 58 311 298 1.853 .54 .49 .484 .489 1.947 12 98 .767 .49 50 2580 5590 44 49 107 112 0 260 153 107 .532 249 97 1.881 .483 -.912 -1.051
7 217 199 151 150 66 49 202 186 154 157 51 36 0 0 89 79 34 43 55 46 34 21 115 87 1.347 .742 .706 .822 1 3.269 52 298 1.002 .39 80 2720 5590 43 51 120 128 -50 196 148 48 .731 183 35 1.367 .695 -.451 -.524
8 460 387 158 165 302 222 486 403 159 166 328 238 0 0 160 132 35 44 90 87 90 81 524 566 1.36 .735 .726 .724 .775 1.588 32 170 .757 .84 60 2870 5590 44 50 136 142 0 381 163 219 .724 397 234 1.381 .715 -.466 -.485
9 1045 886 164 159 881 727 1089 910 164 163 925 751 0 0 222 166 34 46 100 100 100 100 1608 1676 1.212 .825 .812 .851 .872 1.478 32 170 .809 .92 60 3010 5590 44 50 150 156 0 873 157 716 .813 896 740 1.23 .8 -.299 -.322
10 409 354 153 156 256 198 397 368 157 159 244 212 0 0 84 50 34 45 100 100 100 100 454 456 1.293 .773 .869 .789 .81 1.595 12 98 .777 .82 50 3150 5590 44 49 164 169 0 349 154 195 .762 362 209 1.313 .856 -.392 -.225
11 904 1042 159 165 745 877 953 1067 162 172 794 902 0 0 181 153 37 45 100 100 100 100 1622 1696 .849 1.177 1.136 1.215 1.155 1.385 32 230 1.149 .94 70 3300 5590 43 50 178 185 0 1026 163 864 1.16 1051 888 .862 1.119 .214 .162
12 592 687 158 156 434 531 669 717 160 160 511 561 0 0 195 265 36 45 96 100 93 90 965 1072 .817 1.224 1.098 1.194 1.208 2.075 32 170 1.267 .89 60 3450 5590 44 50 194 200 0 677 154 523 1.205 706 553 .83 1.081 .269 .113
13 563 662 162 169 401 493 583 710 167 178 421 541 0 0 171 227 47 75 100 100 100 100 894 962 .813 1.229 1.285 1.215 1.384 1.744 12 80 1.156 .86 50 3590 5570 42 47 208 213 0 652 166 486 1.211 699 533 .826 1.266 .276 .34
14 426 505 157 156 269 349 432 495 161 158 275 339 0 0 135 128 36 46 96 96 87 96 618 614 .771 1.297 1.233 1.45 1.258 2.171 32 170 1.236 .84 60 3740 5590 44 50 223 229 0 497 154 344 1.278 488 334 .783 1.214 .354 .28
15 819 1063 153 152 666 911 862 1118 159 161 709 966 0 0 171 336 36 53 100 96 100 93 1577 1675 .731 1.368 1.362 1.197 1.343 2.093 32 220 1.479 .92 70 3890 5590 43 50 237 244 0 1047 150 897 1.347 1101 952 .742 1.342 .43 .424
16 2657 2152 155 159 2502 1993 2867 2354 159 166 2712 2195 0 0 816 735 37 53 100 100 100 100 4495 4907 1.255 .797 .809 .792 .822 1.53 32 221 .822 .95 70 4030 5580 42 49 251 258 0 2120 157 1963 .785 2319 2162 1.275 .797 -.35 -.327
17 1026 1317 159 163 867 1154 1073 1343 163 170 914 1180 0 0 383 449 73 85 96 100 94 96 2021 2094 .751 1.331 1.291 1.424 1.253 1.701 52 267 1.369 .89 80 4180 5590 43 51 266 274 -100 1297 161 1137 1.311 1323 1162 .763 1.272 .391 .347
18 171 170 154 152 17 18 158 164 161 162 4 12 0 0 57 52 72 67 13 15 1 3 35 16 .944 1.059 3 1.401 1.32 4.879 52 267 -1 -1 80 4320 5590 43 51 280 288 -50 167 150 18 1.043 162 12 .959 2.955 .061 1.563
19 2245 2577 166 162 2079 2415 2411 2910 169 169 2245 2748 0 0 1072 1009 41 50 100 100 100 100 4494 4993 .861 1.162 1.224 1.376 1.185 1.887 32 164 1.082 .94 60 4470 5600 45 51 296 302 0 2538 160 2379 1.144 2866 2707 .874 1.206 .194 .27
20 1192 1051 167 163 1025 888 1193 1051 172 172 1026 888 0 0 205 187 43 60 100 100 100 100 1913 1914 1.154 .866 .865 .863 .873 1.198 80 447 .874 .94 100 4630 5590 42 52 310 320 0 1035 161 875 .853 1035 875 1.172 .853 -.229 -.23

Total number of rows: 43104

Table truncated, full table size 9804 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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