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Sample GSM99369 Query DataSets for GSM99369
Status Public on Mar 08, 2006
Title OV3777_CGH
Sample type genomic
 
Channel 1
Source name XX
Organism Homo sapiens
Characteristics XX
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name OV3777
Organism Homo sapiens
Characteristics OV3777
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44818.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 GPL3523
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
1 317 515 133 166 184 349 300 482 138 169 167 316 0 0 82 109 40 62 100 100 96 100 533 483 .527 1.897 1.892 1.982 1.857 1.672 32 226 2.212 .74 70 1120 8020 38 45 32 39 0 573 185 388 2.11 536 352 .474 2.105 1.077 1.074
2 422 739 129 177 293 562 443 741 137 183 314 564 0 0 95 199 38 60 100 100 100 100 855 878 .521 1.918 1.796 1.89 1.923 1.494 32 170 2.112 .9 60 1270 8000 37 43 48 54 0 822 197 625 2.134 824 627 .469 1.998 1.093 .999
3 1077 1214 133 177 944 1037 1038 1254 137 184 905 1077 0 0 187 255 36 65 100 100 100 100 1981 1982 .91 1.099 1.19 1.083 1.086 1.235 32 220 1.12 .95 70 1410 8010 37 44 61 68 0 1350 197 1154 1.222 1395 1198 .818 1.324 .289 .405
4 268 277 134 167 134 110 251 267 137 168 117 100 0 0 120 128 35 61 73 55 63 46 244 217 1.218 .821 .855 .917 .941 2.869 52 275 1.21 .58 80 1550 8010 37 45 75 83 -50 308 186 122 .913 297 111 1.095 .951 -.131 -.073
5 1561 967 135 179 1426 788 1652 990 139 185 1517 811 0 0 488 276 35 63 100 98 100 98 2214 2328 1.81 .553 .535 .537 .547 1.404 52 295 .544 .95 80 1710 8010 37 45 91 99 0 1076 199 877 .615 1101 902 1.627 .595 -.702 -.75
6 258 313 135 176 123 137 247 293 140 183 112 117 0 0 49 117 41 76 96 65 78 37 260 229 .898 1.114 1.045 .933 .986 3.107 32 164 2.145 .49 60 1850 8010 38 44 106 112 0 348 196 152 1.239 326 130 .807 1.162 .309 .217
7 529 738 131 171 398 567 555 722 134 177 424 551 0 0 134 213 32 63 100 98 98 98 965 975 .702 1.425 1.3 1.353 1.382 1.727 52 297 1.54 .89 80 2000 8000 36 44 120 128 0 821 190 631 1.585 803 613 .631 1.446 .664 .532
8 848 873 131 196 717 677 857 849 145 207 726 653 0 0 192 199 72 104 100 100 100 100 1394 1379 1.059 .944 .899 .941 .984 1.406 32 209 1.017 .88 70 2140 8000 36 43 134 141 0 971 218 753 1.05 944 726 .952 1.001 .071 .001
9 399 436 131 164 268 272 418 426 143 177 287 262 0 0 100 141 76 109 93 93 87 65 540 549 .985 1.015 .913 .933 .997 1.843 32 171 1.175 .77 60 2280 8020 39 45 149 155 0 485 182 303 1.129 474 291 .886 1.015 .175 .022
10 605 715 143 186 462 529 622 704 144 187 479 518 0 0 87 124 35 65 100 100 100 100 991 997 .873 1.145 1.081 1.134 1.144 1.322 32 212 1.232 .89 70 2440 8010 37 44 164 171 0 795 207 588 1.274 783 576 .785 1.203 .349 .267
11 546 471 146 189 400 282 546 472 147 192 400 283 0 0 116 120 35 60 100 96 100 90 682 683 1.418 .705 .708 .654 .654 1.682 32 214 .715 .78 70 2580 8010 37 44 178 185 0 524 210 314 .784 525 315 1.275 .787 -.351 -.346
12 522 451 137 169 385 282 513 452 141 182 376 283 0 0 125 110 32 66 100 100 100 90 667 659 1.365 .732 .753 .714 .699 1.555 32 176 .733 .82 60 2730 8010 38 44 194 200 0 502 188 314 .815 503 315 1.227 .837 -.296 -.256
13 305 439 148 187 157 252 305 451 151 198 157 264 0 0 72 100 41 83 96 93 87 81 409 421 .623 1.605 1.682 1.67 1.827 1.746 32 164 1.811 .73 60 2870 8010 38 44 208 214 0 488 208 280 1.785 502 294 .56 1.871 .836 .903
14 557 744 153 209 404 535 562 739 163 221 409 530 0 0 109 136 52 100 100 100 100 96 939 939 .755 1.324 1.296 1.324 1.24 1.34 32 221 1.366 .87 70 3020 8000 36 43 222 229 0 828 232 595 1.473 822 590 .679 1.441 .559 .528
15 411 655 146 176 265 479 407 684 156 184 261 508 0 0 96 159 60 66 100 100 92 100 744 769 .553 1.808 1.946 1.824 1.784 1.63 52 275 2.026 .82 80 3170 8010 37 45 237 245 0 729 196 533 2.011 761 565 .497 2.165 1.008 1.114
16 3917 2860 142 176 3775 2684 4339 3052 147 179 4197 2876 0 0 1143 758 40 57 100 100 100 100 6459 7073 1.406 .711 .685 .72 .693 1.361 52 276 .695 .97 80 3310 8010 37 45 251 259 0 3181 196 2986 .791 3395 3199 1.264 .762 -.338 -.392
17 626 743 143 168 483 575 611 717 146 171 468 549 0 0 69 157 39 64 100 100 100 100 1058 1017 .84 1.19 1.173 1.16 1.195 1.29 32 221 1.282 .91 70 3460 8010 37 44 266 273 0 827 187 640 1.324 798 611 .755 1.305 .405 .384
18 436 1090 146 157 290 933 444 1088 149 165 298 931 0 0 85 224 38 64 100 100 100 100 1223 1229 .311 3.217 3.124 3.284 3.339 1.279 32 220 3.289 .9 70 3600 8010 37 44 280 287 0 1213 175 1038 3.579 1210 1036 .279 3.475 1.839 1.797
19 1235 2022 141 167 1094 1855 1333 2219 142 178 1192 2052 0 0 531 886 37 60 98 96 98 96 2949 3244 .59 1.696 1.721 1.716 1.69 1.452 52 273 1.714 .96 80 3760 8010 37 45 296 304 0 2249 186 2063 1.886 2468 2283 .53 1.915 .915 .937
20 831 662 148 155 683 507 797 651 149 160 649 496 0 0 166 152 33 59 100 100 100 100 1190 1145 1.347 .742 .764 .73 .722 1.31 32 208 .755 .91 70 3900 8010 37 44 310 317 0 736 172 564 .826 724 552 1.211 .85 -.276 -.234

Total number of rows: 41568

Table truncated, full table size 9415 Kbytes.




Supplementary data files not provided
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