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Sample GSM874864 Query DataSets for GSM874864
Status Public on Dec 20, 2012
Title OV4762_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 OV4762
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 60 years
tumor histology: serous
grade of tumor: 2
event (alive=1, dead=2): 2
progression (no progression=1, progression=2): 2
overall survival (os, n=months): 48.03
progression-free survival (pfs, n=months): 8.75
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/2003-07/43421.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
1 315 312 208 212 107 100 292 289 214 221 84 77 0 0 107 142 46 78 55 50 48 28 207 161 1.07 .935 .917 1.227 1.173 3.121 52 284 1.894 .37 80 2150 8130 81 89 55 63 -50 336 228 108 1.007 311 83 .993 .987 .01 -.018
2 608 709 210 224 398 485 631 657 218 234 421 433 0 0 118 199 44 82 100 100 100 100 883 854 .821 1.219 1.029 1.186 1.24 1.537 12 104 1.435 .81 50 2300 8130 82 87 71 76 0 764 241 522 1.313 708 466 .762 1.108 .393 .148
3 471 387 212 212 259 175 253 261 215 223 41 49 0 0 665 401 46 78 48 36 38 26 434 90 1.48 .676 1.195 1.094 1.211 3.942 52 302 .497 .62 80 2450 8120 80 88 85 93 -50 417 228 189 .728 281 53 1.374 1.287 -.458 .365
4 444 360 225 215 219 145 461 339 221 218 236 124 0 0 115 97 43 63 91 83 91 41 364 360 1.51 .662 .525 .595 .642 1.798 12 104 .898 .57 50 2600 8130 82 87 101 106 0 388 232 156 .713 365 134 1.402 .566 -.488 -.821
5 772 675 215 217 557 458 743 633 217 222 528 416 0 0 317 264 46 82 100 90 100 81 1015 944 1.216 .822 .788 .783 .838 2.241 32 170 .796 .74 60 2750 8140 83 89 116 122 0 727 234 493 .886 682 448 1.129 .849 -.175 -.237
6 387 704 215 214 172 490 415 719 221 220 200 505 0 0 104 231 51 84 81 96 75 90 662 705 .351 2.849 2.525 2.8 2.729 2.021 32 160 3.273 .73 60 2890 8140 83 89 130 136 0 758 231 528 3.069 775 544 .326 2.72 1.618 1.444
7 307 273 212 211 95 62 267 253 215 220 55 42 0 0 119 102 47 80 51 40 38 19 157 97 1.532 .653 .764 1.007 .775 3.899 52 281 1.304 .39 80 3030 8120 80 88 143 151 -50 294 227 67 .703 273 45 1.422 .823 -.508 -.282
8 611 589 209 203 402 386 607 555 211 214 398 352 0 0 138 220 42 79 100 93 96 81 788 750 1.041 .96 .884 .862 .84 1.766 32 164 1.091 .78 60 3180 8130 82 88 159 165 0 635 219 416 1.034 598 379 .967 .953 .049 -.07
9 857 694 208 209 649 485 910 682 209 218 702 473 0 0 229 202 43 78 100 100 100 94 1134 1175 1.338 .747 .674 .724 .783 1.702 52 329 .752 .83 90 3330 8130 80 89 172 181 0 748 225 522 .805 735 510 1.242 .726 -.313 -.462
10 399 328 217 216 182 112 388 315 216 220 171 99 0 0 68 103 45 80 100 62 100 34 294 270 1.625 .615 .579 .605 .812 2.35 32 198 1.298 .4 70 3470 8130 81 88 187 194 0 353 233 121 .663 339 107 1.508 .624 -.593 -.681
11 864 621 207 203 657 418 911 591 212 211 704 388 0 0 237 176 44 84 100 100 100 96 1075 1092 1.572 .636 .551 .624 .635 1.654 52 325 .69 .8 90 3620 8130 80 89 201 210 0 669 219 450 .685 637 418 1.459 .594 -.545 -.752
12 579 564 211 204 368 360 584 559 215 211 373 355 0 0 126 161 45 71 100 100 98 92 728 728 1.022 .978 .952 .946 .987 1.788 52 254 1.076 .79 80 3770 8130 81 89 217 225 0 608 220 388 1.054 602 382 .949 1.025 .076 .036
13 662 769 211 212 451 557 672 781 214 222 461 569 0 0 165 233 48 80 100 100 98 98 1008 1030 .81 1.235 1.234 1.211 1.322 1.556 52 340 1.335 .88 90 3910 8130 80 89 230 239 0 828 228 600 1.33 841 613 .752 1.33 .412 .411
14 440 521 216 236 224 285 445 476 224 245 229 240 0 0 121 188 51 100 93 90 81 68 509 469 .786 1.272 1.048 1.157 1.264 2.02 32 181 1.687 .68 70 4080 8120 80 87 248 255 0 561 254 307 1.371 513 259 .73 1.129 .455 .175
15 831 1314 208 216 623 1098 826 1303 228 234 618 1087 0 0 147 260 258 186 100 100 76 100 1721 1705 .567 1.762 1.759 1.763 1.782 1.304 80 381 1.435 .83 110 4200 8130 79 90 258 269 0 1416 233 1183 1.899 1404 1171 .527 1.895 .925 .922
16 5756 4533 208 238 5548 4295 5568 4001 245 260 5360 3763 0 0 3775 2987 364 251 98 98 96 94 9843 9123 1.292 .774 .702 .749 .78 1.58 52 188 .789 .94 80 4350 8150 83 91 275 283 0 4883 256 4627 .834 4310 4054 1.199 .756 -.262 -.403
17 1394 1541 212 236 1182 1305 1467 1485 219 247 1255 1249 0 0 458 516 53 99 100 99 100 99 2487 2504 .906 1.104 .995 1.101 1.098 1.382 120 447 1.097 .95 120 4490 8130 79 91 287 299 0 1660 254 1406 1.189 1600 1345 .841 1.072 .25 .1
18 224 233 217 229 7 4 227 231 224 243 10 2 0 0 40 75 54 95 7 11 0 1 11 12 1.75 .571 .2 1.382 1.551 4.142 52 227 5.631 .27 80 4640 8120 80 88 304 312 -50 251 247 4 .616 249 2 1.625 .215 -.7 -2.215
19 5723 4810 215 213 5508 4597 5865 4807 221 229 5650 4594 0 0 960 798 61 95 100 100 100 100 10105 10244 1.198 .835 .813 .835 .847 1.159 80 363 .833 .98 110 4780 8130 79 90 316 327 0 5182 229 4952 .899 5178 4949 1.112 .876 -.153 -.191
20 827 837 211 231 616 606 803 802 222 242 592 571 0 0 221 232 70 101 100 100 100 98 1222 1163 1.017 .984 .965 .975 .996 1.49 80 356 1.004 .85 110 4920 8130 79 90 330 341 0 902 249 653 1.06 864 615 .944 1.039 .084 .055

Total number of rows: 43104

Table truncated, full table size 9732 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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