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Sample GSM874795 Query DataSets for GSM874795
Status Public on Dec 20, 2012
Title OV5025-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 OV5025
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): 54.77
progression-free survival (pfs, n=months): 16.32
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/2003-08/43529.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
1 353 472 155 278 198 194 349 469 155 275 194 191 0 0 51 72 36 55 100 96 100 93 392 385 1.021 .98 .985 1.008 1.039 1.515 32 158 1.116 .69 60 1920 8250 54 60 57 63 0 568 335 233 1.179 564 230 .848 1.185 .238 .245
2 692 903 149 280 543 623 679 917 152 281 530 637 0 0 123 129 39 53 100 100 100 100 1166 1167 .872 1.147 1.202 1.154 1.134 1.273 32 216 1.123 .93 70 2070 8250 53 60 71 78 0 1087 337 750 1.381 1104 767 .724 1.446 .466 .533
3 513 604 144 278 369 326 520 603 148 281 376 325 0 0 171 108 37 54 100 100 96 96 695 701 1.132 .883 .864 .968 .844 1.829 32 164 .83 .82 60 2220 8250 54 60 87 93 0 727 335 392 1.063 726 391 .94 1.04 .089 .057
4 330 426 146 271 184 155 324 435 151 273 178 164 0 0 94 78 39 51 90 90 87 71 339 342 1.187 .842 .921 .827 .877 1.964 32 164 .868 .71 60 2370 8250 54 60 102 108 0 513 326 187 1.014 524 197 .986 1.109 .02 .149
5 1114 1076 157 271 957 805 1160 1165 160 266 1003 894 0 0 320 357 36 52 100 96 100 96 1762 1897 1.189 .841 .891 .764 .839 1.541 32 170 .881 .93 60 2510 8250 54 60 116 122 0 1295 326 969 1.012 1402 1076 .988 1.073 .018 .101
6 455 600 154 268 301 332 473 602 154 274 319 334 0 0 137 123 37 52 100 100 93 100 633 653 .907 1.103 1.047 1.172 1.203 1.524 32 164 1.079 .86 60 2650 8250 54 60 130 136 0 722 323 400 1.327 725 402 .753 1.26 .409 .334
7 386 418 145 265 241 153 376 417 150 268 231 152 0 0 92 85 37 49 96 90 93 68 394 383 1.575 .635 .658 .554 .66 1.967 32 164 .673 .65 60 2800 8250 54 60 145 151 0 503 319 184 .764 502 183 1.309 .792 -.388 -.337
8 730 737 141 272 589 465 713 763 145 281 572 491 0 0 151 142 31 53 100 100 100 100 1054 1063 1.267 .789 .858 .774 .835 1.399 32 164 .769 .9 60 2940 8250 54 60 159 165 0 887 327 560 .95 918 591 1.052 1.033 -.074 .047
9 1105 1661 149 276 956 1385 1095 1703 153 276 946 1427 0 0 224 351 36 51 100 100 100 100 2341 2373 .69 1.449 1.508 1.434 1.48 1.231 52 325 1.487 .96 90 3090 8240 51 60 172 181 0 1999 332 1667 1.744 2050 1717 .574 1.815 .802 .86
10 317 372 149 267 168 105 307 372 153 269 158 105 0 0 73 72 35 50 96 78 90 51 273 263 1.6 .625 .665 .61 .716 2.04 52 242 .753 .58 80 3240 8240 52 60 188 196 0 448 321 126 .752 448 126 1.329 .8 -.411 -.322
11 968 1038 150 269 818 769 969 1059 152 270 819 790 0 0 209 157 38 50 100 100 100 100 1587 1609 1.064 .94 .965 .958 .932 1.414 52 285 .902 .93 90 3380 8250 52 61 201 210 0 1249 324 925 1.131 1275 951 .884 1.161 .178 .215
12 507 604 147 276 360 328 510 609 151 276 363 333 0 0 99 113 35 53 100 98 100 98 688 696 1.098 .911 .917 .875 .874 1.527 52 254 .932 .86 80 3530 8240 52 60 217 225 0 727 332 395 1.097 733 401 .912 1.104 .133 .143
13 666 783 147 275 519 508 657 787 151 278 510 512 0 0 139 149 36 56 100 100 100 100 1027 1022 1.022 .979 1.004 .965 .953 1.315 52 301 .99 .91 90 3670 8240 51 60 230 239 0 942 331 611 1.178 947 616 .849 1.208 .236 .273
14 531 462 149 269 382 193 540 479 159 275 391 210 0 0 158 133 58 59 100 82 90 75 575 601 1.979 .505 .537 .502 .547 1.642 52 325 .615 .82 90 3820 8230 50 59 245 254 0 556 324 232 .608 576 253 1.645 .646 -.718 -.63
15 1047 1043 152 272 895 771 1034 1050 159 278 882 778 0 0 156 141 52 56 100 100 100 100 1666 1660 1.161 .861 .882 .859 .875 1.242 80 400 .851 .94 110 3970 8240 50 61 259 270 0 1255 327 928 1.037 1264 936 .965 1.062 .052 .086
16 3035 2876 154 263 2881 2613 3041 2957 156 265 2887 2694 0 0 987 816 51 73 100 100 100 100 5494 5581 1.103 .907 .933 .918 .874 1.257 52 254 .896 .96 90 4110 8250 52 61 274 283 0 3461 317 3145 1.092 3559 3242 .916 1.123 .126 .167
17 1562 1378 155 256 1407 1122 1588 1363 169 266 1433 1107 0 0 299 282 78 86 100 100 100 100 2529 2540 1.254 .797 .773 .789 .814 1.206 80 397 .828 .96 110 4260 8230 49 60 288 299 0 1658 308 1350 .96 1640 1332 1.042 .93 -.059 -.105
18 161 264 170 263 -9 1 158 270 176 272 -12 7 0 0 46 57 69 69 7 9 0 0 -8 -5 null null null 1.044 1.228 2.269 52 236 7.774 .08 80 4400 8220 50 58 304 312 -50 318 317 1 null 325 8 null null null null
19 7074 5667 156 264 6918 5403 6715 5500 161 268 6559 5236 0 0 1280 1088 47 57 100 100 100 100 12321 11795 1.28 .781 .798 .777 .791 1.151 80 376 .785 .98 110 4550 8240 50 61 317 328 0 6820 318 6503 .94 6619 6302 1.064 .961 -.089 -.058
20 979 1062 145 251 834 811 967 1051 154 255 822 800 0 0 221 186 49 58 100 100 100 100 1645 1622 1.028 .972 .973 .981 .98 1.261 80 334 1.021 .94 110 4690 8240 50 61 331 342 0 1278 302 976 1.17 1265 963 .854 1.171 .227 .228

Total number of rows: 43104

Table truncated, full table size 9701 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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