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Sample GSM874848 Query DataSets for GSM874848
Status Public on Dec 20, 2012
Title OV4455_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 OV4455
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 61 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): 55.86
progression-free survival (pfs, n=months): 32.24
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4000B
Description Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44825.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 GPL3523
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
1 452 407 170 176 282 231 448 370 191 242 278 194 0 0 150 185 217 635 62 3 9 0 513 472 1.221 .819 .698 .809 .93 2.368 32 214 .949 .6 70 1430 7750 51 58 31 38 0 477 206 271 .961 434 227 1.041 .818 -.058 -.289
2 600 709 176 175 424 534 608 714 181 193 432 539 0 0 132 268 58 101 100 96 96 87 958 971 .794 1.259 1.248 1.239 1.345 1.604 32 171 1.481 .76 60 1570 7750 52 58 46 52 0 831 205 626 1.477 837 632 .677 1.463 .563 .549
3 942 882 175 163 767 719 912 876 178 183 737 713 0 0 395 358 43 101 93 96 93 96 1486 1450 1.067 .937 .967 1.019 .966 2.071 32 176 .934 .86 60 1720 7750 52 58 61 67 0 1034 191 843 1.099 1027 836 .91 1.134 .137 .182
4 362 307 182 186 180 121 314 254 200 226 132 68 0 0 210 198 148 222 48 23 17 7 301 200 1.488 .672 .515 .813 .92 3.255 52 287 1.071 .58 80 1870 7740 50 58 75 83 -50 360 218 142 .788 298 80 1.269 .604 -.343 -.727
5 1773 1136 169 200 1604 936 1786 1112 181 211 1617 912 0 0 416 436 61 110 100 96 100 96 2540 2529 1.714 .584 .564 .562 .57 1.407 32 214 .601 .9 70 2020 7740 50 57 90 97 0 1332 235 1098 .684 1304 1069 1.461 .661 -.547 -.596
6 480 733 168 196 312 537 455 691 175 206 287 495 0 0 144 303 49 105 100 90 96 87 849 782 .581 1.721 1.725 1.574 1.684 1.761 32 166 2.099 .81 60 2150 7740 51 57 104 110 0 860 230 630 2.018 810 580 .495 2.023 1.013 1.016
7 858 938 175 182 683 756 826 900 177 199 651 718 0 0 206 305 45 107 100 100 100 100 1439 1369 .903 1.107 1.103 1.067 1.177 1.614 32 230 1.22 .8 70 2300 7730 49 56 118 125 0 1100 213 887 1.298 1055 842 .77 1.293 .376 .371
8 1144 1086 173 185 971 901 1128 1006 179 204 955 821 0 0 279 308 52 116 100 100 100 100 1872 1776 1.078 .928 .86 .922 .886 1.344 32 222 .919 .89 70 2450 7730 49 56 133 140 0 1274 217 1057 1.088 1180 963 .919 1.008 .122 .012
9 510 424 169 178 341 246 568 386 175 194 399 208 0 0 275 232 51 104 76 69 65 50 587 607 1.386 .721 .521 .855 .7 3.068 52 300 .837 .72 80 2600 7740 50 58 148 156 -50 497 209 288 .846 453 244 1.182 .611 -.241 -.71
10 847 1061 180 192 667 869 855 1068 184 207 675 876 0 0 258 364 55 113 96 100 96 93 1536 1551 .768 1.303 1.298 1.304 1.3 1.617 32 208 1.373 .84 70 2750 7750 51 58 163 170 0 1244 225 1019 1.528 1252 1027 .655 1.522 .611 .606
11 660 418 188 189 472 229 677 381 192 231 489 192 0 0 189 201 56 184 100 53 96 21 701 681 2.061 .485 .393 .4 .501 2.753 32 173 .509 .44 60 2890 7750 52 58 178 184 0 490 222 269 .569 447 225 1.758 .46 -.814 -1.119
12 430 412 188 207 242 205 436 378 189 235 248 171 0 0 234 232 52 160 67 51 57 26 447 419 1.18 .847 .69 .929 .939 3.904 52 290 1.553 .51 80 3040 7740 50 58 192 200 -50 483 243 240 .993 443 201 1.007 .809 -.01 -.307
13 430 533 197 206 233 327 417 510 207 229 220 304 0 0 132 229 68 125 90 78 75 68 560 524 .713 1.403 1.382 1.13 1.669 2.634 32 164 1.83 .67 60 3180 7740 51 57 207 213 0 625 242 383 1.646 598 356 .608 1.62 .719 .696
14 839 943 200 235 639 708 844 920 206 264 644 685 0 0 159 293 60 141 100 100 100 96 1347 1329 .903 1.108 1.064 1.052 1.071 1.575 32 165 1.286 .79 60 3340 7740 51 57 223 229 0 1106 276 830 1.299 1079 803 .77 1.247 .378 .319
15 544 584 182 206 362 378 540 604 190 219 358 398 0 0 111 173 56 121 100 93 100 75 740 756 .958 1.044 1.112 .958 1.086 1.991 32 224 1.444 .64 70 3480 7750 51 58 236 243 0 685 242 443 1.224 708 467 .817 1.304 .292 .383
16 4810 2719 179 201 4631 2518 5291 2947 203 229 5112 2746 0 0 1516 940 95 135 100 100 100 100 7149 7858 1.839 .544 .537 .527 .519 1.394 32 226 .528 .96 70 3620 7740 50 57 250 257 0 3188 236 2953 .638 3456 3220 1.568 .63 -.649 -.667
17 538 556 174 199 364 357 592 528 186 221 418 329 0 0 245 308 66 122 82 75 78 59 721 747 1.02 .981 .787 .872 1.011 3.581 52 294 1.303 .69 80 3770 7740 50 58 265 273 -50 652 233 419 1.15 619 386 .869 .923 .202 -.116
18 588 747 177 198 411 549 590 635 185 211 413 437 0 0 204 342 57 120 96 96 93 81 960 850 .749 1.336 1.058 1.262 1.236 1.577 32 176 1.611 .8 60 3920 7740 51 57 281 287 0 876 232 644 1.566 745 512 .638 1.241 .647 .311
19 1623 1554 172 200 1451 1354 1633 1594 179 228 1461 1394 0 0 489 574 57 173 100 96 100 93 2805 2855 1.072 .933 .954 .868 .903 1.495 32 176 .955 .94 60 4060 7740 51 57 295 301 0 1822 235 1588 1.094 1869 1635 .914 1.119 .13 .162
20 637 564 188 214 449 350 565 469 194 235 377 255 0 0 413 339 60 133 73 75 63 48 799 632 1.283 .78 .676 .88 .759 2.353 52 288 .826 .78 80 4210 7730 49 57 309 317 -50 661 251 410 .914 550 299 1.094 .793 -.13 -.334

Total number of rows: 41568

Table truncated, full table size 9380 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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