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Sample GSM99361 Query DataSets for GSM99361
Status Public on Mar 08, 2006
Title OV3782_CGH
Sample type genomic
 
Channel 1
Source name XX
Organism Homo sapiens
Characteristics XX
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name OV3782
Organism Homo sapiens
Characteristics OV3782
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45077.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 GPL3332
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
1 677 547 286 184 391 363 656 552 291 190 370 368 0 0 116 134 61 78 100 100 100 96 754 738 1.077 .928 .995 .899 .878 1.567 52 345 .802 .67 90 2190 7820 37 46 34 43 0 532 179 353 .903 537 358 1.107 .967 -.147 -.048
2 875 548 285 171 590 377 879 512 293 181 594 341 0 0 164 191 61 79 100 98 100 84 967 935 1.565 .639 .574 .574 .612 1.735 52 232 .678 .8 80 2330 7830 39 47 49 57 0 533 166 367 .622 498 332 1.609 .558 -.686 -.841
3 755 612 295 186 460 426 747 578 301 193 452 392 0 0 137 175 80 83 100 100 100 98 886 844 1.08 .926 .867 .893 .87 1.514 52 312 .935 .76 90 2470 7820 37 46 62 71 0 595 181 414 .901 562 381 1.11 .844 -.151 -.245
4 786 385 292 176 494 209 772 386 295 184 480 210 0 0 139 116 64 74 100 90 100 63 703 690 2.364 .423 .438 .399 .447 1.886 52 267 .358 .62 90 2600 7830 38 47 75 84 0 374 171 203 .412 375 204 2.43 .426 -1.281 -1.233
5 1407 1228 283 176 1124 1052 1248 1187 316 194 965 1011 0 0 426 367 182 111 100 100 100 100 2176 1976 1.068 .936 1.048 .936 .985 1.366 80 341 .907 .91 100 2750 7830 38 48 90 100 0 1194 171 1023 .91 1155 983 1.098 1.019 -.135 .027
6 758 518 280 179 478 339 753 495 279 184 473 316 0 0 104 138 56 74 100 98 100 96 817 789 1.41 .709 .668 .67 .664 1.613 52 215 .731 .79 80 2900 7830 39 47 106 114 0 504 174 330 .69 481 307 1.45 .65 -.536 -.622
7 1143 1054 285 174 858 880 1042 960 287 183 757 786 0 0 382 314 65 76 100 100 100 100 1738 1543 .975 1.026 1.038 1.048 1.043 1.418 80 360 .943 .9 110 3050 7830 37 48 119 130 0 1025 169 856 .998 934 765 1.002 1.01 -.003 .014
8 999 855 275 175 724 680 951 819 300 209 676 644 0 0 212 219 158 173 100 100 100 97 1404 1320 1.065 .939 .953 .927 .942 1.402 80 365 .915 .88 110 3190 7830 37 48 133 144 0 832 170 661 .914 797 626 1.095 .927 -.13 -.11
9 763 536 264 167 499 369 751 541 288 205 487 374 0 0 136 153 173 199 96 84 92 42 868 861 1.352 .739 .768 .703 .684 1.762 52 245 .689 .75 80 3350 7820 38 46 151 159 0 521 162 359 .719 526 364 1.39 .747 -.475 -.421
10 1248 992 266 174 982 818 1229 942 320 263 963 768 0 0 287 286 344 461 100 90 84 26 1800 1731 1.2 .833 .798 .816 .818 1.368 52 288 .81 .91 90 3480 7830 38 47 163 172 0 965 169 796 .81 916 747 1.234 .776 -.304 -.366
11 746 609 255 169 491 440 741 571 260 176 486 402 0 0 133 167 55 73 100 100 100 96 931 888 1.116 .896 .827 .858 .94 1.62 80 379 .907 .8 100 3640 7830 38 48 179 189 0 592 164 428 .872 555 391 1.147 .805 -.198 -.314
12 591 553 250 171 341 382 610 512 255 179 360 341 0 0 93 181 57 73 100 100 100 93 723 701 .893 1.12 .947 1.044 1.173 1.857 32 172 1.225 .69 70 3790 7830 39 46 195 202 0 538 166 372 1.09 498 332 .918 .921 .124 -.118
13 705 548 244 165 461 383 685 555 248 171 441 390 0 0 151 171 56 72 100 98 100 92 844 831 1.204 .831 .884 .778 .865 1.732 80 390 .894 .79 110 3930 7830 37 48 207 218 0 533 160 373 .808 540 379 1.237 .86 -.307 -.217
14 911 949 243 158 668 791 945 984 244 169 702 826 0 0 328 356 56 82 92 98 91 91 1459 1528 .845 1.184 1.177 1.256 1.176 1.779 120 485 1.163 .91 130 4090 7820 35 48 222 235 0 923 154 769 1.152 957 803 .868 1.145 .204 .195
15 503 559 232 162 271 397 488 534 250 188 256 372 0 0 129 183 93 115 96 95 76 85 668 628 .683 1.465 1.453 1.395 1.431 1.951 120 462 1.634 .72 130 4200 7830 36 49 233 246 0 544 158 386 1.425 519 362 .702 1.413 .511 .499
16 2045 2260 221 166 1824 2094 2010 2221 240 184 1789 2055 0 0 428 652 94 113 100 100 100 100 3918 3844 .871 1.148 1.149 1.127 1.095 1.283 80 405 1.165 .94 110 4360 7820 36 47 250 261 0 2198 161 2037 1.117 2160 1999 .896 1.117 .159 .16
17 834 898 201 150 633 748 810 877 207 163 609 727 0 0 259 316 63 91 100 100 100 97 1381 1336 .846 1.182 1.194 1.152 1.195 1.607 80 366 1.183 .85 100 4520 7820 37 47 267 277 0 873 146 728 1.149 853 707 .87 1.161 .201 .216
18 1024 929 197 148 827 781 984 910 202 166 787 762 0 0 177 204 60 98 100 100 100 100 1608 1549 1.059 .944 .968 .932 .996 1.351 52 278 .908 .87 90 4670 7820 37 46 282 291 0 904 144 760 .919 885 741 1.089 .942 -.123 -.087
19 1209 1245 206 144 1003 1101 1185 1237 205 158 979 1093 0 0 406 427 51 76 98 100 97 98 2104 2072 .911 1.098 1.116 1.092 1.085 1.476 80 344 1.108 .88 100 4800 7830 38 48 295 305 0 1211 140 1071 1.068 1203 1063 .937 1.086 .095 .119
20 651 550 198 143 453 407 648 523 202 153 450 380 0 0 119 187 47 69 100 100 100 96 860 830 1.113 .898 .844 .826 .826 1.635 52 230 .949 .83 80 4960 7830 39 47 312 320 0 535 139 396 .874 509 370 1.144 .821 -.194 -.284

Total number of rows: 41568

Table truncated, full table size 9175 Kbytes.




Supplementary data files not provided
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