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Sample GSM72085 Query DataSets for GSM72085
Status Public on Aug 27, 2005
Title ovca41-LMP
Sample type RNA
 
Channel 1
Source name UHR
Organism Homo sapiens
Characteristics UHR
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name ovca41-LMP Total RNA
Organism Homo sapiens
Characteristics ovca41-LMP Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31216.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 Aug 26, 2005
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 GPL2790
Series (1)
GSE3208 Distinction between serous tumors of low malignant potential and serous 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
1 940 3511 228 555 712 2956 981 3742 294 622 753 3187 0 0 317 879 183 453 98 100 86 96 3668 3940 .241 4.152 4.232 1 1 1 52 197 1 .82 90 2050 8410 76 85 0 9 0 6270 991 5279 7.414 6682 5691 .135 7.558 2.89 2.918
2 3393 1410 230 531 3163 879 3350 1422 300 557 3120 891 0 0 941 501 184 328 100 85 100 63 4042 4011 3.598 .278 .286 1 1 1 120 466 1 .66 120 2210 8420 76 88 15 27 0 2518 948 1570 .496 2539 1591 2.015 .51 -1.011 -.972
3 10666 3697 226 499 10440 3198 10704 3469 252 509 10478 2970 0 0 6164 1821 100 178 100 98 100 96 13638 13448 3.265 .306 .283 1 1 1 52 205 1 .95 80 2350 8430 79 87 31 39 0 6602 891 5711 .547 6195 5304 1.828 .506 -.87 -.982
4 1370 1379 238 515 1132 864 1276 1255 284 537 1038 740 0 0 553 588 122 177 100 94 100 80 1996 1778 1.31 .763 .713 1 1 1 52 237 1 .85 80 2490 8410 77 85 45 53 0 2463 920 1543 1.363 2241 1321 .734 1.273 .447 .348
5 639 1327 224 507 415 820 654 1294 236 525 430 787 0 0 121 304 75 173 100 98 100 96 1235 1217 .506 1.976 1.83 1 1 1 52 314 1 .81 90 2630 8410 76 85 58 67 0 2370 905 1464 3.528 2311 1405 .283 3.268 1.819 1.709
6 692 2938 213 519 479 2419 686 2916 215 537 473 2397 0 0 93 643 38 281 100 100 100 100 2898 2870 .198 5.05 5.068 1 1 1 52 313 1 .9 90 2780 8420 77 86 73 82 0 5246 927 4320 9.018 5207 4280 .111 9.049 3.173 3.178
7 11582 19158 225 539 11357 18619 11707 19469 239 600 11482 18930 0 0 2036 3697 66 414 100 100 100 100 29976 30412 .61 1.639 1.649 1 1 1 52 305 1 .95 90 2920 8410 76 85 87 96 0 34211 963 33248 2.928 34766 33804 .342 2.944 1.55 1.558
8 3023 3518 222 530 2801 2988 2985 3477 234 571 2763 2947 0 0 877 992 66 335 100 100 100 100 5789 5710 .937 1.067 1.067 1 1 1 52 328 1 .92 90 3070 8410 76 85 102 111 0 6282 946 5336 1.905 6209 5263 .525 1.905 .93 .93
9 897 1054 215 519 682 535 913 1004 218 568 698 485 0 0 167 265 42 295 100 81 100 37 1217 1183 1.275 .784 .695 1 1 1 32 159 1 .67 60 3220 8410 78 84 119 125 0 1882 927 955 1.401 1793 866 .714 1.241 .486 .311
10 293 544 224 550 69 -6 237 514 225 584 13 -36 0 0 178 198 44 254 30 9 19 3 63 -23 null null null 1 1 1 52 268 1 .04 80 3360 8410 77 85 132 140 -50 971 982 -11 null 918 null null null null null
11 3024 1626 210 566 2814 1060 3299 1598 221 617 3089 1032 0 0 905 537 55 257 100 94 100 80 3874 4121 2.655 .377 .334 1 1 1 52 247 1 .81 80 3510 8410 77 85 147 155 0 2904 1011 1893 .673 2854 1843 1.487 .597 -.572 -.745
12 1951 3012 208 594 1743 2418 2186 2901 223 692 1978 2307 0 0 836 1301 59 427 100 96 96 88 4161 4285 .721 1.387 1.166 1 1 1 80 323 1 .86 100 3660 8420 77 87 161 171 0 5379 1061 4318 2.477 5180 4120 .404 2.083 1.309 1.058
13 847 896 209 595 638 301 897 846 229 652 688 251 0 0 201 267 82 424 100 32 96 3 939 939 2.12 .472 .365 1 1 1 52 233 1 .46 80 3800 8400 76 84 176 184 0 1600 1063 538 .842 1511 448 1.187 .651 -.247 -.618
14 8445 3883 215 604 8230 3279 9234 3951 306 682 9019 3347 0 0 2371 994 715 435 100 100 100 98 11509 12366 2.51 .398 .371 1 1 1 52 313 1 .93 90 3940 8400 75 84 189 198 0 6934 1079 5855 .711 7055 5977 1.406 .663 -.491 -.594
15 3428 3959 215 640 3213 3319 3687 3949 308 717 3472 3309 0 0 788 912 700 440 100 100 96 100 6532 6781 .968 1.033 .953 1 1 1 52 332 1 .93 90 4090 8400 75 84 204 213 0 7070 1143 5927 1.845 7052 5909 .542 1.702 .883 .767
16 733 776 210 633 523 143 772 763 220 649 562 130 0 0 160 209 86 239 98 34 96 3 666 692 3.657 .273 .231 1 1 1 52 312 1 .37 90 4240 8410 76 85 219 228 0 1386 1130 255 .488 1363 232 2.048 .413 -1.034 -1.276
17 549 806 246 675 303 131 538 822 333 700 292 147 0 0 99 228 183 235 88 30 23 5 434 439 2.313 .432 .503 1 1 1 52 275 1 .41 80 4380 8410 77 85 234 242 -50 1439 1205 234 .772 1468 263 1.295 .899 -.373 -.154
18 2403 1001 250 665 2153 336 2523 967 335 709 2273 302 0 0 453 270 187 243 100 62 100 31 2489 2575 6.408 .156 .133 1 1 1 80 416 1 .44 110 4540 8410 75 86 248 259 0 1788 1188 600 .279 1727 539 3.588 .237 -1.843 -2.075
19 2242 1507 245 595 1997 912 2443 1494 280 623 2198 899 0 0 578 415 121 221 100 96 100 84 2909 3097 2.19 .457 .409 1 1 1 52 266 1 .79 90 4670 8400 75 84 262 271 0 2691 1063 1629 .816 2668 1605 1.226 .73 -.294 -.453
20 4918 1817 274 535 4644 1282 5356 1762 346 558 5082 1227 0 0 1251 431 373 221 100 100 100 98 5926 6309 3.622 .276 .241 1 1 1 52 293 1 .89 90 4810 8400 75 84 276 285 0 3245 955 2289 .493 3146 2191 2.029 .431 -1.02 -1.214

Total number of rows: 43008

Table truncated, full table size 9328 Kbytes.




Supplementary data files not provided
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