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Sample GSM96061 Query DataSets for GSM96061
Status Public on Feb 25, 2006
Title Ovarian Ca OV10
Sample type RNA
 
Channel 1
Source name CRG Reference
Organism Homo sapiens
Characteristics CRG Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ovarian Ca OV10_CHTN
Organism Homo sapiens
Characteristics Ovarian Ca OV10_CHTN
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13898.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 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 GPL3147
Series (2)
GSE4198 Ovarian cancers
GSE4268 Breast and ovarian carcinoma

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 919 1036 112 298 807 738 840 803 116 314 728 505 0 0 308 917 31 150 100 78 100 67 1545 1233 1.093 .914 .694 .598 .702 2.827 52 327 1.656 .6 90 800 8660 109 118 63 72 0 2513 723 1790 2.218 1948 1225 .451 1.683 1.149 .751 1.149
2 652 975 112 298 540 677 331 715 117 314 219 417 0 0 651 824 32 157 87 65 68 56 1217 636 .798 1.254 1.904 1.393 1.255 3.484 32 199 1.5 .67 70 950 8650 109 116 79 86 0 2365 723 1642 3.041 1734 1012 .329 4.619 1.605 2.208 1.605
3 5858 1202 118 289 5740 913 5655 1166 120 305 5537 877 0 0 1415 466 30 157 100 94 100 94 6653 6414 6.287 .159 .158 .152 .157 1.61 52 312 .166 .78 90 1080 8650 108 117 91 100 0 2916 701 2215 .386 2828 2127 2.592 .384 -1.374 -1.38 -1.374
4 482 534 116 291 366 243 247 382 117 314 131 91 0 0 431 399 31 162 78 43 62 34 609 222 1.506 .664 .695 .916 .93 4.261 32 200 1.064 .57 70 1220 8650 109 116 106 113 0 1295 706 589 1.611 927 221 .621 1.685 .688 .753 .688
5 2337 763 116 304 2221 459 2267 764 116 332 2151 460 0 0 257 232 27 165 100 94 100 65 2680 2611 4.839 .207 .214 .183 .203 1.844 52 294 .21 .65 90 1360 8660 109 118 119 128 0 1851 737 1113 .501 1853 1116 1.995 .519 -.996 -.947 -.996
6 424 838 110 340 314 498 189 523 113 355 79 183 0 0 433 741 30 158 62 50 56 46 812 262 .631 1.586 2.316 3.24 3.203 5.832 32 199 2.609 .54 70 1490 8650 109 116 133 140 0 2033 825 1208 3.847 1269 444 .26 5.619 1.944 2.49 1.944
7 2401 1175 118 333 2283 842 2446 1108 122 349 2328 775 0 0 458 401 30 164 100 98 100 94 3125 3103 2.711 .369 .333 .332 .345 1.696 52 245 .374 .75 80 1630 8660 110 118 147 155 0 2850 808 2042 .895 2688 1880 1.118 .808 -.161 -.308 -.161
8 1119 672 121 316 998 356 1108 653 129 345 987 337 0 0 173 274 66 166 100 73 100 50 1354 1324 2.803 .357 .341 .295 .368 2.274 52 258 .346 .52 90 1760 8670 110 119 159 168 0 1630 767 864 .865 1584 817 1.156 .828 -.209 -.272 -.209
9 2357 693 116 330 2241 363 2145 658 123 355 2029 328 0 0 1227 264 35 160 100 83 100 58 2604 2357 6.174 .162 .162 .162 .155 2.212 12 95 .113 .46 50 1880 8670 112 117 173 178 0 1681 800 881 .393 1596 796 2.545 .392 -1.348 -1.351 -1.348
10 459 534 115 333 344 201 447 522 120 355 332 189 0 0 121 166 31 158 100 55 100 23 545 521 1.711 .584 .569 .54 .595 2.542 52 261 1.234 .38 80 2030 8660 110 118 187 195 0 1295 808 488 1.417 1266 458 .706 1.381 .503 .466 .503
11 4202 1848 123 329 4079 1519 3929 1840 125 349 3806 1511 0 0 1153 756 31 166 100 96 100 92 5598 5317 2.685 .372 .397 .323 .334 1.939 52 282 .382 .85 90 2170 8660 109 118 200 209 0 4483 798 3685 .903 4463 3665 1.107 .963 -.147 -.054 -.147
12 524 542 125 336 399 206 482 565 134 356 357 229 0 0 135 152 52 165 100 65 100 21 605 586 1.937 .516 .641 .523 .61 2.22 32 184 1.135 .37 70 2290 8670 111 118 213 220 0 1315 815 500 1.252 1371 555 .798 1.556 .325 .638 .325
13 623 634 123 328 500 306 605 611 128 356 482 283 0 0 175 270 43 177 100 69 100 38 806 765 1.634 .612 .587 .532 .635 2.825 52 252 1.032 .55 80 2440 8670 111 119 228 236 0 1538 796 742 1.485 1482 686 .674 1.424 .57 .51 .57
14 1187 1162 118 318 1069 844 1201 1141 122 352 1083 823 0 0 273 331 32 177 100 98 100 96 1913 1906 1.267 .79 .76 .754 .729 1.593 52 267 .784 .81 90 2580 8670 110 119 241 250 0 2819 771 2047 1.915 2768 1996 .522 1.843 .937 .882 .937
15 1456 908 124 334 1332 574 1394 888 132 375 1270 554 0 0 447 284 41 194 100 93 100 78 1906 1824 2.321 .431 .436 .393 .441 1.866 32 177 .42 .68 70 2710 8660 110 117 255 262 0 2203 810 1392 1.045 2154 1344 .957 1.058 .064 .082 .064
16 2617 1504 126 345 2491 1159 2788 1574 134 374 2662 1229 0 0 691 605 50 181 100 93 100 87 3650 3891 2.149 .465 .462 .425 .496 1.792 80 372 .478 .83 100 2850 8660 109 119 268 278 0 3648 837 2811 1.129 3818 2981 .886 1.12 .175 .163 .175
17 1128 640 124 342 1004 298 1127 634 127 365 1003 292 0 0 270 305 31 178 100 63 100 42 1302 1295 3.369 .297 .291 .33 .355 2.062 52 222 .376 .55 80 3000 8660 110 118 284 292 0 1552 830 723 .72 1538 708 1.389 .706 -.474 -.502 -.474
18 873 494 116 360 757 134 860 469 123 375 744 109 0 0 142 205 33 169 100 44 100 17 891 853 5.649 .177 .147 .252 .305 2.137 52 227 .276 .29 90 3130 8670 110 119 296 305 0 1198 873 325 .429 1138 264 2.329 .355 -1.22 -1.493 -1.22
19 510 1685 114 356 396 1329 504 1672 120 357 390 1316 0 0 100 397 33 154 100 100 100 100 1725 1706 .298 3.356 3.374 3.323 3.198 1.394 52 200 3.91 .86 80 3260 8670 111 119 310 318 0 4087 864 3224 8.141 4056 3192 .123 8.185 3.025 3.033 3.025
20 2472 849 124 369 2348 480 2466 817 129 372 2342 448 0 0 484 244 38 167 100 90 100 65 2828 2790 4.892 .204 .191 .18 .204 1.724 52 235 .208 .76 80 3400 8660 110 118 324 332 0 2059 895 1164 .496 1982 1087 2.017 .464 -1.012 -1.108 -1.012

Total number of rows: 44160

Table truncated, full table size 10009 Kbytes.




Supplementary data files not provided
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