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Sample GSM99358 Query DataSets for GSM99358
Status Public on Mar 08, 2006
Title OV3654_CGH
Sample type genomic
 
Channel 1
Source name XX
Organism Homo sapiens
Characteristics XX
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name OV3654
Organism Homo sapiens
Characteristics OV3654
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs//43880.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) [email protected]
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
1 244 271 106 143 138 128 244 285 111 157 138 142 0 0 29 80 31 54 100 75 100 58 266 280 1.078 .928 1.029 .736 .977 2.368 12 90 1.099 .69 50 1810 6010 46 51 54 59 0 364 192 172 1.245 382 191 .803 1.381 .316 .466
2 250 276 110 140 140 136 229 280 112 152 119 140 0 0 69 64 26 48 100 100 91 58 276 259 1.029 .971 1.176 .983 1.024 1.881 12 90 1.193 .63 50 1960 6010 46 51 69 74 0 370 188 183 1.304 376 188 .767 1.579 .383 .659
3 139 184 108 161 31 23 119 171 111 164 11 10 0 0 69 77 27 51 32 32 23 11 54 21 1.348 .742 .909 2.097 2.355 3.535 52 294 2.374 .31 80 2110 6030 47 55 83 91 -50 247 216 31 .996 229 13 1.004 1.22 -.006 .287
4 155 192 103 144 52 48 145 175 106 148 42 31 0 0 51 98 24 44 59 36 46 15 100 73 1.083 .923 .738 .917 .867 3.742 52 264 4.692 .22 80 2250 6030 47 55 97 105 -50 258 193 64 1.239 235 42 .807 .99 .309 -.014
5 393 496 105 152 288 344 389 471 107 155 284 319 0 0 135 182 24 43 100 100 96 93 632 603 .837 1.194 1.123 1.173 1.226 1.987 32 171 1.334 .8 60 2400 6030 48 54 113 119 0 666 204 462 1.603 632 428 .624 1.507 .681 .592
6 178 189 104 149 74 40 160 184 107 151 56 35 0 0 68 55 23 41 75 44 59 23 114 91 1.85 .541 .625 .758 .741 3.037 52 287 .908 .45 80 2540 6020 46 54 126 134 -50 254 200 54 .725 247 47 1.379 .839 -.463 -.254
7 131 148 105 132 26 16 114 128 107 138 9 -4 0 0 59 68 22 44 34 23 25 15 42 5 1.625 .615 null 1.161 1.322 4.855 52 296 2.247 .34 80 2690 6020 46 54 141 149 -50 199 177 21 .826 172 -5 1.211 null -.276 null
8 291 413 111 151 180 262 268 402 114 155 157 251 0 0 103 111 32 51 91 100 83 83 442 408 .687 1.456 1.599 1.66 1.72 1.783 12 104 1.732 .67 50 2830 6030 48 53 156 161 0 554 203 352 1.953 539 337 .512 2.145 .966 1.101
9 677 877 109 164 568 713 739 900 111 166 630 736 0 0 226 169 22 47 100 100 100 100 1281 1366 .797 1.255 1.168 1.378 1.231 1.765 32 236 1.129 .85 70 2980 6030 47 54 170 177 0 1177 220 957 1.685 1208 988 .594 1.568 .752 .649
10 251 254 106 146 145 108 253 242 111 155 147 96 0 0 65 86 39 47 96 78 81 50 253 243 1.343 .745 .653 .787 .929 2.432 32 170 1.031 .55 60 3130 6020 47 53 186 192 0 341 196 145 1 325 129 1 .876 -.001 -.19
11 592 642 112 162 480 480 606 630 140 398 494 468 0 0 150 107 311 2953 90 0 15 0 960 962 1 1 .947 1.098 .991 1.863 32 232 .914 .86 70 3270 6030 47 54 199 206 0 862 217 644 1.342 845 628 .745 1.271 .424 .346
12 434 668 111 159 323 509 480 651 113 162 369 492 0 0 152 240 24 48 100 96 93 93 832 861 .635 1.576 1.333 1.591 1.508 1.801 32 170 1.696 .88 60 3420 6020 47 53 215 221 0 896 213 683 2.115 874 660 .473 1.789 1.08 .839
13 394 541 107 156 287 385 405 550 109 160 298 394 0 0 162 213 23 49 100 87 96 87 672 692 .745 1.341 1.322 1.292 1.221 2.244 32 170 1.383 .83 60 3570 6020 47 53 230 236 0 726 209 517 1.8 738 529 .555 1.774 .848 .827
14 315 388 112 156 203 232 328 379 113 158 216 223 0 0 70 110 24 48 100 96 100 84 435 439 .875 1.143 1.032 1.05 1.031 1.666 32 170 1.317 .81 60 3710 6020 47 53 244 250 0 521 209 311 1.534 509 299 .652 1.385 .617 .47
15 558 814 119 162 439 652 571 893 116 164 452 731 0 0 124 260 25 49 100 96 100 93 1091 1183 .673 1.485 1.617 1.328 1.451 1.607 32 170 1.658 .88 60 3860 6020 47 53 259 265 0 1092 217 875 1.993 1198 981 .502 2.17 .995 1.118
16 2129 2617 119 167 2010 2450 2228 2785 119 176 2109 2618 0 0 759 824 28 55 100 100 100 100 4460 4727 .82 1.219 1.241 1.278 1.293 1.63 32 228 1.196 .92 70 4000 6020 46 53 272 279 0 3512 224 3288 1.636 3737 3513 .611 1.666 .71 .736
17 797 1039 120 175 677 864 821 1074 125 183 701 899 0 0 256 276 33 56 98 98 98 98 1541 1600 .784 1.276 1.282 1.294 1.326 1.317 52 333 1.416 .88 90 4160 6020 45 54 287 296 0 1394 235 1159 1.713 1441 1206 .584 1.721 .776 .783
18 127 181 129 180 -2 1 122 172 137 193 -7 -8 0 0 32 50 43 67 9 9 1 3 -1 -15 null null null 1.605 1.909 3.247 52 273 6.28 .2 80 4290 6020 46 54 301 309 -50 243 242 1 null 231 -11 null null null null
19 1861 2536 136 189 1725 2347 1993 2963 146 204 1857 2774 0 0 666 922 40 74 100 100 100 100 4072 4631 .735 1.361 1.494 1.318 1.341 1.459 32 159 1.395 .91 60 4450 6030 48 54 318 324 0 3403 254 3150 1.826 3976 3723 .548 2.005 .869 1.003
20 783 913 133 185 650 728 793 950 142 192 660 765 0 0 132 234 41 60 100 98 100 98 1378 1425 .893 1.12 1.159 1.042 1.131 1.741 80 497 1.205 .9 110 4600 6020 44 55 330 341 0 1225 248 977 1.503 1275 1027 .665 1.555 .588 .637

Total number of rows: 43104

Table truncated, full table size 9605 Kbytes.




Supplementary data files not provided
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