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Sample GSM874862 Query DataSets for GSM874862
Status Public on Dec 20, 2012
Title OV4704_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 OV4704
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 70 years
tumor histology: IIIC
grade of tumor: 3
event (alive=1, dead=2): 2
progression (no progression=1, progression=2): 2
overall survival (os, n=months): 43.65
progression-free survival (pfs, n=months): 24.05
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/2003-07/43094.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
1 324 271 149 180 175 91 326 260 155 188 177 80 0 0 47 88 31 87 100 50 91 25 266 257 1.923 .52 .452 .576 .608 2.61 12 98 2.227 .34 50 2120 9110 56 61 53 58 0 296 197 99 .568 284 87 1.761 .494 -.816 -1.018
2 426 312 160 168 266 144 452 308 162 183 292 140 0 0 96 118 31 84 100 75 100 41 410 432 1.847 .541 .479 .453 .53 3.017 12 104 .643 .55 50 2280 9110 56 61 69 74 0 341 183 157 .591 336 153 1.691 .524 -.758 -.933
3 221 333 160 185 61 148 183 273 162 194 23 88 0 0 112 178 34 86 42 50 38 34 209 111 .412 2.426 3.826 1.77 1.775 3.071 52 268 2.771 .54 80 2410 9110 55 63 81 89 -50 364 202 162 2.65 298 96 .377 4.179 1.406 2.063
4 241 206 157 187 84 19 210 195 159 201 53 8 0 0 88 84 38 86 59 21 38 1 103 61 4.421 .226 .151 .772 1.167 5.79 52 275 7.432 .08 80 2560 9110 55 63 96 104 -50 225 204 21 .247 213 9 4.048 .165 -2.017 -2.601
5 439 510 154 174 285 336 474 523 157 194 320 349 0 0 184 168 32 131 87 84 84 62 621 669 .848 1.179 1.091 1.402 1.129 2.899 32 164 1.582 .6 60 2710 9120 57 63 112 118 0 557 190 367 1.288 571 381 .777 1.191 .365 .252
6 339 284 158 183 181 101 336 275 162 197 178 92 0 0 96 108 32 83 93 53 84 21 282 270 1.792 .558 .517 .52 .531 3.287 32 166 .953 .36 60 2860 9110 56 62 127 133 0 310 200 110 .609 300 100 1.641 .564 -.714 -.825
7 211 234 161 182 50 52 199 206 164 192 38 24 0 0 68 125 33 87 51 28 36 13 102 62 .962 1.04 .632 1.236 1.63 4.243 52 280 7.161 .21 80 3000 9100 54 62 140 148 -50 256 199 57 1.136 225 26 .88 .69 .184 -.536
8 398 387 158 184 240 203 417 353 162 194 259 169 0 0 101 140 34 92 96 81 93 46 443 428 1.182 .846 .653 .84 .9 1.784 32 164 1.225 .71 60 3150 9110 56 62 156 162 0 423 201 222 .924 386 185 1.082 .713 -.114 -.489
9 505 517 163 191 342 326 500 518 164 197 337 327 0 0 122 166 40 85 100 94 100 78 668 664 1.049 .953 .97 .896 .964 1.841 52 242 1.14 .8 80 3300 9110 55 63 170 178 0 565 209 356 1.041 566 357 .961 1.06 .058 .084
10 225 217 160 194 65 23 208 211 162 195 48 17 0 0 56 85 34 80 61 26 40 3 88 65 2.826 .354 .354 1.31 1.302 3.821 52 244 4.578 .21 80 3430 9100 54 62 183 191 -50 237 212 25 .386 230 19 2.588 .387 -1.372 -1.37
11 506 331 156 178 350 153 514 316 160 188 358 138 0 0 99 118 33 81 100 73 100 44 503 496 2.288 .437 .385 .374 .468 2.276 52 323 .601 .56 90 3590 9110 54 63 198 207 0 362 194 167 .477 345 151 2.095 .421 -1.067 -1.248
12 295 404 156 181 139 223 276 392 161 190 120 211 0 0 64 151 37 77 98 86 88 61 362 331 .623 1.604 1.758 1.348 1.375 2.676 52 256 3.144 .5 80 3740 9100 54 62 214 222 0 441 198 244 1.752 428 230 .571 1.92 .809 .941
13 410 299 156 181 254 118 412 296 159 191 256 115 0 0 75 87 35 85 100 57 100 26 372 371 2.153 .465 .449 .407 .431 2.299 52 290 .817 .48 90 3880 9110 54 63 227 236 0 327 198 129 .507 323 126 1.971 .491 -.979 -1.027
14 216 273 149 197 67 76 201 249 152 214 52 52 0 0 67 150 35 104 59 25 42 9 143 104 .882 1.134 1 1.559 1.796 4.089 52 236 -1 -1 80 4020 9100 54 62 242 250 -50 298 215 83 1.239 272 57 .807 1.092 .309 .127
15 511 556 154 178 357 378 412 445 156 190 258 267 0 0 500 703 35 90 100 86 100 65 735 525 .944 1.059 1.035 .86 1.097 2.161 80 353 1.536 .83 110 4170 9110 53 64 255 266 -100 607 194 413 1.156 486 292 .865 1.13 .21 .177
16 2444 3432 155 202 2289 3230 2289 2790 270 291 2134 2588 0 0 1718 2530 558 517 80 92 75 84 5519 4722 .709 1.411 1.213 1.54 1.397 1.939 52 203 1.36 .94 80 4300 9120 56 64 270 278 -100 3748 221 3528 1.541 3047 2827 .649 1.325 .624 .405
17 635 555 152 198 483 357 625 551 209 257 473 353 0 0 158 190 396 371 73 42 1 1 840 826 1.353 .739 .746 .675 .714 1.766 80 416 .765 .9 110 4460 9100 52 63 284 295 -100 606 216 390 .807 602 386 1.239 .815 -.309 -.295
18 162 201 149 180 13 21 162 190 152 200 13 10 0 0 34 84 35 89 28 17 3 5 34 23 .619 1.615 .769 2.18 1.639 4.085 52 226 81.102 .03 80 4600 9090 53 61 300 308 -50 220 197 23 1.764 208 11 .567 .84 .819 -.251
19 1798 1842 147 190 1651 1652 1796 1802 158 227 1649 1612 0 0 330 458 64 327 100 100 100 100 3303 3261 .999 1.001 .978 .984 .995 1.207 80 367 1.043 .95 110 4750 9100 52 63 313 324 0 2012 208 1804 1.093 1968 1761 .915 1.068 .128 .094
20 319 353 149 202 170 151 318 345 162 243 169 143 0 0 83 122 65 329 87 5 66 1 321 312 1.126 .888 .846 .757 .818 2.898 80 367 2.363 .42 110 4890 9100 52 63 327 338 0 386 221 165 .97 377 156 1.031 .924 -.044 -.114

Total number of rows: 43104

Table truncated, full table size 9532 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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