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Sample GSM99362 Query DataSets for GSM99362
Status Public on Mar 08, 2006
Title OV3887_CGH
Sample type genomic
 
Channel 1
Source name XX
Organism Homo sapiens
Characteristics XX
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name OV3887
Organism Homo sapiens
Characteristics OV3887
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43136.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 Mar 07, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3528
Series (1)
GSE4405 High-resolution gene copy number and expression profiling of human chromosome 22 in ovarian 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
1 532 760 164 367 368 393 536 751 168 379 372 384 0 0 151 212 38 100 100 93 96 87 761 756 .936 1.068 1.032 1.056 1 2.012 32 170 1.221 .73 60 1780 5770 46 52 51 57 0 1038 501 537 1.459 1026 525 .686 1.41 .545 .496
2 643 833 175 379 468 454 643 810 180 388 468 431 0 0 153 220 36 89 100 91 100 91 922 899 1.031 .97 .921 .901 1 1.777 12 98 1.026 .78 50 1920 5760 45 50 65 70 0 1138 518 620 1.325 1106 589 .755 1.258 .406 .331
3 231 463 170 390 61 73 176 409 175 419 6 19 0 0 170 212 41 146 25 25 19 13 134 25 .836 1.197 3.167 2.157 2 3.344 52 306 1.956 .55 80 2070 5770 45 53 79 87 -50 632 533 100 1.635 559 26 .612 4.325 .709 2.113
4 468 704 170 385 298 319 413 691 171 388 243 306 0 0 190 187 36 104 100 91 100 58 617 549 .934 1.07 1.259 1.088 1.143 2.344 12 104 1.308 .64 50 2210 5780 47 52 94 99 0 962 526 436 1.462 944 418 .684 1.72 .548 .782
5 955 1147 159 375 796 772 897 1224 165 388 738 849 0 0 409 338 33 96 100 93 100 93 1568 1587 1.031 .97 1.15 .981 .969 2.236 32 170 1.01 .86 60 2360 5770 46 52 109 115 -100 1567 512 1054 1.325 1672 1160 .755 1.571 .406 .652
6 367 558 153 357 214 201 355 561 156 368 202 204 0 0 140 121 33 93 90 81 81 59 415 406 1.065 .939 1.01 1.115 .943 2.795 32 155 1.001 .58 60 2510 5760 45 51 124 130 0 762 488 275 1.283 766 279 .779 1.379 .359 .464
7 259 481 155 375 104 106 201 455 157 380 46 80 0 0 137 133 39 96 53 46 38 26 210 126 .981 1.019 1.739 1.458 1.376 2.71 52 280 1.768 .45 80 2650 5770 45 53 137 145 -50 657 512 145 1.392 621 109 .718 2.375 .477 1.248
8 426 651 165 363 261 288 234 503 164 370 69 140 0 0 326 366 34 100 59 59 50 44 549 209 .906 1.103 2.029 1.718 1.348 2.609 52 277 1.226 .83 80 2800 5770 45 53 152 160 -50 889 496 393 1.507 687 191 .663 2.771 .592 1.471
9 1290 1682 167 363 1123 1319 1456 1875 170 370 1289 1512 0 0 529 561 38 103 93 93 93 93 2442 2801 .851 1.175 1.173 1.239 1.158 2.225 32 155 1.159 .91 60 2950 5760 45 51 168 174 0 2297 496 1802 1.604 2561 2065 .623 1.602 .682 .68
10 350 443 168 372 182 71 283 445 171 381 115 73 0 0 188 113 37 99 63 34 55 15 253 188 2.563 .39 .635 .621 .573 4.1 52 282 .542 .43 80 3090 5770 45 53 181 189 -50 605 508 97 .533 608 100 1.877 .867 -.908 -.206
11 1406 1110 169 385 1237 725 1447 1155 172 400 1278 770 0 0 223 195 38 131 100 100 100 96 1962 2048 1.706 .586 .603 .568 .599 1.401 32 230 .605 .89 70 3240 5770 45 52 196 203 0 1516 526 990 .801 1578 1052 1.249 .823 -.321 -.281
12 799 1166 168 377 631 789 879 1265 170 375 711 888 0 0 293 249 41 90 100 100 91 100 1420 1599 .8 1.25 1.249 1.437 1.265 1.734 12 90 1.163 .9 50 3380 5750 44 49 211 216 0 1593 515 1078 1.708 1728 1213 .586 1.706 .772 .771
13 752 736 164 362 588 374 840 759 164 369 676 397 0 0 291 207 31 98 96 90 96 78 962 1073 1.572 .636 .587 .696 .655 1.862 32 160 .633 .76 60 3530 5760 45 51 226 232 0 1005 494 511 .869 1037 542 1.151 .802 -.203 -.318
14 737 679 161 353 576 326 733 696 161 362 572 343 0 0 98 132 33 95 100 100 100 83 902 915 1.767 .566 .6 .533 .518 1.57 12 98 .615 .61 50 3670 5760 45 50 240 245 0 927 482 445 .773 951 469 1.294 .819 -.371 -.288
15 1121 1467 161 364 960 1103 1163 1489 161 375 1002 1125 0 0 352 351 33 96 100 100 100 100 2063 2127 .87 1.149 1.123 1.184 1.145 1.593 32 170 1.15 .89 60 3820 5770 46 52 255 261 0 2004 497 1507 1.569 2034 1537 .637 1.534 .65 .617
16 3040 3332 157 370 2883 2962 3139 3379 162 374 2982 3009 0 0 1141 1288 34 88 100 100 100 100 5845 5991 .973 1.027 1.009 .991 1.018 1.587 32 224 1.058 .94 70 3970 5760 44 51 269 276 0 4551 505 4046 1.403 4615 4110 .713 1.378 .489 .463
17 1585 2069 160 353 1425 1716 1661 2184 166 357 1501 1831 0 0 585 746 39 94 100 98 100 96 3141 3332 .83 1.204 1.22 1.199 1.175 1.953 52 329 1.309 .91 90 4120 5760 43 52 283 292 -100 2826 482 2344 1.645 2983 2501 .608 1.666 .718 .737
18 184 377 167 354 17 23 159 361 174 369 -8 7 0 0 95 107 46 98 11 15 9 5 40 -1 .739 1.353 null 1.178 2.026 5.489 52 277 8.352 .15 80 4260 5760 44 52 298 306 -50 515 484 31 1.848 493 10 .541 null .886 null
19 3690 4820 177 370 3513 4450 4212 5442 182 385 4035 5072 0 0 1449 1831 49 100 100 100 100 100 7963 9107 .789 1.267 1.257 1.203 1.291 1.67 32 166 1.299 .94 60 4410 5770 46 52 314 320 -100 6584 505 6078 1.73 7433 6928 .578 1.717 .791 .78
20 2056 3197 172 368 1884 2829 2054 3200 184 388 1882 2832 0 0 343 576 96 117 100 100 100 100 4713 4714 .666 1.502 1.505 1.498 1.487 1.234 80 453 1.543 .95 100 4560 5760 43 53 327 337 0 4367 503 3864 2.051 4371 3868 .488 2.055 1.036 1.039

Total number of rows: 43104

Table truncated, full table size 9793 Kbytes.




Supplementary data files not provided
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