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Sample GSM99371 Query DataSets for GSM99371
Status Public on Mar 08, 2006
Title OV3097_CGH
Sample type genomic
 
Channel 1
Source name XX
Organism Homo sapiens
Characteristics XX
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name OV3097
Organism Homo sapiens
Characteristics OV3097
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44610.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
1 247 396 120 187 127 209 247 364 124 194 127 177 0 0 49 132 28 65 100 90 93 65 336 304 .608 1.646 1.394 1.535 1.883 2.204 32 158 2.926 .58 60 1280 8600 65 71 53 59 0 501 237 264 2.081 460 224 .48 1.763 1.058 .818
2 332 584 123 169 209 415 344 570 124 176 221 401 0 0 73 191 26 60 100 93 96 93 624 622 .504 1.986 1.814 1.844 2.266 2.056 32 171 2.454 .8 60 1430 8590 64 70 68 74 0 739 214 525 2.511 721 507 .398 2.295 1.329 1.198
3 501 512 125 177 376 335 527 505 126 183 402 328 0 0 148 136 27 65 100 100 96 96 711 730 1.122 .891 .816 .921 .917 1.697 32 165 .924 .84 60 1570 8590 64 70 82 88 0 648 224 424 1.127 639 415 .887 1.032 .172 .045
4 183 234 125 182 58 52 185 235 127 191 60 53 0 0 60 86 28 67 63 42 51 13 110 113 1.115 .897 .883 1.264 1.25 4.06 52 254 2.978 .37 80 1710 8580 62 70 95 103 -50 296 230 66 1.134 297 67 .882 1.117 .181 .16
5 852 835 120 169 732 666 835 827 126 174 715 658 0 0 179 159 51 62 100 100 100 100 1398 1373 1.099 .91 .92 .911 .897 1.374 32 215 .872 .86 70 1860 8590 63 70 110 117 0 1056 214 842 1.151 1046 832 .869 1.164 .203 .219
6 191 352 113 175 78 177 185 309 116 180 72 134 0 0 70 181 27 63 69 71 55 55 255 206 .441 2.269 1.861 2.2 2.667 3.031 52 287 3.402 .65 80 2000 8580 62 70 124 132 -50 445 221 224 2.87 391 169 .348 2.354 1.521 1.235
7 337 538 120 184 217 354 353 533 123 190 233 349 0 0 129 224 29 64 94 94 90 78 571 582 .613 1.631 1.498 1.628 1.616 1.993 52 279 1.785 .82 80 2150 8590 63 71 139 147 0 680 233 448 2.063 674 441 .485 1.895 1.045 .922
8 605 681 144 173 461 508 643 657 147 181 499 484 0 0 125 124 38 62 100 100 100 100 969 983 .907 1.102 .97 1.119 1.198 1.433 32 213 1.133 .86 70 2290 8580 62 69 153 160 0 861 219 643 1.394 831 612 .717 1.227 .479 .295
9 297 301 146 186 151 115 292 278 150 189 146 92 0 0 110 131 33 64 84 57 69 46 266 238 1.313 .762 .63 .815 .869 2.039 52 289 1.177 .64 80 2440 8580 62 70 168 176 -50 381 235 145 .963 352 116 1.038 .797 -.054 -.327
10 600 892 154 188 446 704 625 914 158 195 471 726 0 0 131 276 30 63 100 100 100 96 1150 1197 .634 1.578 1.541 1.509 1.663 1.606 32 165 1.698 .88 60 2590 8590 64 70 184 190 0 1128 238 890 1.996 1156 918 .501 1.95 .997 .963
11 451 581 153 185 298 396 436 568 157 193 283 383 0 0 131 197 35 68 96 93 96 90 694 666 .753 1.329 1.353 1.183 1.373 2.678 32 225 1.494 .82 70 2740 8590 63 70 198 205 0 735 234 501 1.681 718 484 .595 1.712 .749 .775
12 280 302 144 181 136 121 237 260 146 188 93 79 0 0 142 148 33 65 67 53 53 42 257 172 1.124 .89 .849 1.14 1.02 2.33 52 266 1.111 .71 80 2880 8570 61 69 212 220 -50 382 229 153 1.125 329 100 .889 1.074 .17 .104
13 217 333 136 182 81 151 210 322 141 185 74 140 0 0 81 172 34 62 57 63 53 51 232 214 .536 1.864 1.892 1.947 2.222 2.074 52 258 2.847 .62 80 3020 8570 61 69 226 234 -50 421 230 191 2.358 407 177 .424 2.393 1.237 1.259
14 533 862 149 196 384 666 554 825 153 212 405 629 0 0 114 239 37 86 100 100 96 100 1050 1034 .577 1.734 1.553 1.732 1.676 1.368 32 212 1.9 .87 70 3160 8580 62 69 240 247 0 1090 248 842 2.194 1043 796 .456 1.964 1.133 .974
15 337 532 147 219 190 313 321 516 153 228 174 297 0 0 80 142 39 78 100 96 96 87 503 471 .607 1.647 1.707 1.612 1.555 1.881 32 170 2.104 .67 60 3320 8580 63 69 257 263 0 673 277 396 2.084 653 376 .48 2.159 1.059 1.11
16 2865 3252 140 211 2725 3041 3180 3345 158 244 3040 3134 0 0 804 865 126 177 100 100 100 100 5766 6174 .896 1.116 1.031 1.115 1.09 1.327 32 232 1.069 .95 70 3460 8570 61 68 270 277 0 4113 267 3846 1.411 4231 3964 .708 1.304 .497 .383
17 392 664 123 193 269 471 388 646 126 197 265 453 0 0 133 225 27 65 100 100 90 96 740 718 .571 1.751 1.709 1.857 1.904 1.615 32 176 1.897 .86 60 3610 8580 63 69 286 292 0 840 244 596 2.215 817 573 .452 2.162 1.147 1.112
18 444 914 122 205 322 709 461 967 123 210 339 762 0 0 142 327 28 68 96 100 90 96 1031 1101 .454 2.202 2.248 2.309 2.225 1.963 32 222 2.341 .88 70 3750 8580 62 69 299 306 0 1156 259 897 2.785 1223 964 .359 2.843 1.478 1.507
19 907 1392 122 180 785 1212 946 1537 124 190 824 1357 0 0 327 571 27 67 100 100 96 100 1997 2181 .648 1.544 1.647 1.582 1.572 1.766 32 176 1.611 .92 60 3900 8580 63 69 315 321 0 1761 228 1533 1.953 1944 1716 .512 2.083 .966 1.059
20 545 711 115 184 430 527 588 745 117 189 473 561 0 0 192 261 26 57 96 96 96 90 957 1034 .816 1.226 1.186 1.272 1.158 1.89 32 170 1.299 .91 60 4050 8580 63 69 330 336 0 899 233 667 1.55 942 710 .645 1.5 .632 .585

Total number of rows: 41568

Table truncated, full table size 9212 Kbytes.




Supplementary data files not provided
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