NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM874880 Query DataSets for GSM874880
Status Public on Dec 20, 2012
Title OV4936_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 OV4936
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 54 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): 46.81
progression-free survival (pfs, n=months): 17.73
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/2003-08/43879.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 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
1 317 409 141 254 176 155 323 424 143 253 182 170 0 0 87 80 30 65 100 84 93 56 331 352 1.135 .881 .934 .849 .836 2.286 32 164 1.059 .57 60 1780 5560 57 63 51 57 0 590 367 224 1.271 612 245 .787 1.348 .346 .431
2 332 487 136 245 196 242 327 485 139 249 191 240 0 0 64 107 37 61 100 100 100 91 438 431 .81 1.235 1.257 1.18 1.271 1.735 12 104 1.707 .69 50 1920 5560 57 62 65 70 0 703 354 349 1.782 700 346 .561 1.814 .834 .859
3 176 324 142 268 34 56 148 297 149 274 6 29 0 0 74 136 55 74 23 32 15 11 90 35 .607 1.647 4.833 2.319 2.168 3.875 52 302 3.945 .39 80 2070 5560 56 64 79 87 -50 468 387 81 2.378 429 42 .421 6.978 1.25 2.803
4 195 318 135 240 60 78 166 306 138 253 31 66 0 0 92 98 32 72 48 48 32 19 138 97 .769 1.3 2.129 1.567 1.446 2.615 52 276 2.101 .46 80 2220 5560 56 64 94 102 -50 459 346 113 1.877 442 95 .533 3.074 .908 1.62
5 561 722 132 233 429 489 578 754 134 243 446 521 0 0 171 254 30 68 100 96 100 93 918 967 .877 1.14 1.168 1.046 1.1 1.553 32 164 1.236 .87 60 2370 5560 57 63 110 116 0 1042 336 706 1.646 1089 752 .608 1.686 .719 .754
6 216 331 138 263 78 68 200 340 140 262 62 77 0 0 73 103 30 67 67 59 51 21 146 139 1.147 .872 1.242 1.279 1.453 2.764 52 279 2.757 .34 80 2510 5560 56 64 123 131 -50 478 380 98 1.259 491 111 .795 1.793 .332 .842
7 181 285 140 263 41 22 154 257 141 266 14 -6 0 0 67 120 31 68 38 25 32 11 63 8 1.864 .537 null 1.193 1.467 3.854 52 294 3.814 .41 80 2660 5560 56 64 138 146 -50 411 380 32 .775 371 -9 1.291 null -.368 null
8 450 679 146 270 304 409 467 684 153 274 321 414 0 0 118 213 53 71 100 91 91 91 713 735 .743 1.345 1.29 1.221 1.2 1.468 12 104 1.471 .83 50 2810 5570 58 63 154 159 0 980 390 590 1.942 987 598 .515 1.862 .958 .897
9 945 954 149 266 796 688 948 972 154 273 799 706 0 0 187 199 33 74 100 100 100 100 1484 1505 1.157 .864 .884 .847 .878 1.312 32 170 .866 .91 60 2950 5560 57 63 168 174 0 1377 384 993 1.248 1403 1019 .801 1.276 .319 .351
10 383 522 151 256 232 266 387 517 156 256 236 261 0 0 61 116 35 65 100 91 100 91 498 497 .872 1.147 1.106 .994 1.124 1.8 12 98 1.34 .79 50 3090 5550 56 61 182 187 0 754 370 384 1.655 746 377 .604 1.597 .727 .675
11 870 807 157 268 713 539 904 814 159 274 747 546 0 0 136 133 35 72 100 100 100 100 1252 1293 1.323 .756 .731 .745 .791 1.268 32 236 .746 .89 70 3240 5560 56 63 196 203 0 1165 387 778 1.091 1175 788 .916 1.055 .126 .078
12 605 996 154 263 451 733 589 1022 153 271 435 759 0 0 119 167 35 73 100 100 100 100 1184 1194 .615 1.625 1.745 1.633 1.604 1.262 12 98 1.663 .89 50 3380 5550 56 61 211 216 0 1438 380 1058 2.346 1475 1096 .426 2.519 1.23 1.333
13 580 867 143 251 437 616 626 823 148 258 483 572 0 0 120 291 34 74 100 100 100 100 1053 1055 .709 1.41 1.184 1.305 1.376 1.588 12 90 1.598 .84 50 3530 5540 55 60 226 231 0 1252 362 889 2.035 1188 826 .491 1.71 1.025 .774
14 448 708 148 246 300 462 468 738 149 251 320 492 0 0 104 192 31 73 96 96 96 93 762 812 .649 1.54 1.538 1.492 1.568 1.735 32 160 1.688 .88 60 3680 5550 56 62 241 247 0 1022 355 667 2.223 1065 710 .45 2.22 1.153 1.15
15 695 921 144 261 551 660 726 928 147 270 582 667 0 0 207 266 32 75 100 96 96 96 1211 1249 .835 1.198 1.146 1.207 1.172 1.328 32 221 1.239 .91 70 3820 5550 55 62 254 261 0 1330 377 953 1.729 1340 963 .578 1.655 .79 .726
16 2746 2437 154 259 2592 2178 2901 2622 158 262 2747 2363 0 0 848 681 36 84 100 100 100 100 4770 5110 1.19 .84 .86 .859 .851 1.317 32 170 .835 .97 60 3970 5550 56 62 270 276 0 3518 374 3144 1.213 3785 3411 .824 1.242 .279 .312
17 975 1075 149 256 826 819 1053 1094 169 275 904 838 0 0 404 406 135 137 90 92 86 88 1645 1742 1.009 .992 .927 .995 .957 2.006 52 285 .986 .91 80 4120 5560 56 64 284 292 -100 1552 370 1182 1.431 1579 1210 .699 1.338 .517 .42
18 158 266 152 269 6 -3 149 265 175 294 -3 -4 0 0 50 77 140 146 1 1 0 0 3 -7 null null null 2.64 2 3.838 52 265 3.682 .42 80 4260 5560 56 64 298 306 -50 384 388 -4 null 383 -6 null null null null
19 2298 2460 163 277 2135 2183 2464 2875 170 279 2301 2598 0 0 1022 986 57 85 96 96 96 96 4318 4899 .978 1.022 1.129 1.065 1.023 1.391 32 170 1.005 .96 60 4410 5550 56 62 314 320 0 3551 400 3152 1.476 4151 3751 .677 1.63 .562 .705
20 1003 1423 161 265 842 1158 1012 1421 167 274 851 1156 0 0 164 256 54 82 100 100 100 100 2000 2007 .727 1.375 1.358 1.366 1.353 1.284 80 524 1.405 .94 110 4570 5550 53 64 327 338 0 2054 383 1672 1.985 2051 1669 .504 1.961 .989 .972

Total number of rows: 43104

Table truncated, full table size 9623 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap