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Sample GSM72081 Query DataSets for GSM72081
Status Public on Aug 27, 2005
Title ovca22-LMP
Sample type RNA
 
Channel 1
Source name UHR
Organism Homo sapiens
Characteristics UHR
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name ovca22-LMP Total RNA
Organism Homo sapiens
Characteristics ovca22-LMP Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31205.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
1 732 1343 184 273 548 1070 742 1311 190 283 558 1038 0 0 119 308 45 102 100 100 100 100 1618 1596 .512 1.953 1.86 1 1 1 52 306 1 .9 90 2240 8030 78 87 103 112 0 1509 307 1202 2.194 1473 1166 .456 2.09 1.133 1.064
2 594 3782 194 281 400 3501 609 4072 206 287 415 3791 0 0 132 1148 99 109 96 100 91 100 3901 4206 .114 8.753 9.135 1 1 1 80 308 1 .95 100 2380 8030 78 88 117 127 0 4249 316 3934 9.834 4575 4260 .102 10.264 3.298 3.36
3 3192 2017 199 293 2993 1724 3103 2058 238 310 2904 1765 0 0 799 489 177 144 100 100 100 100 4717 4669 1.736 .576 .608 1 1 1 120 507 1 .91 130 2530 8030 76 89 130 143 0 2266 329 1937 .647 2312 1983 1.545 .683 -.628 -.55
4 8159 7154 189 317 7970 6837 8134 7494 213 336 7945 7177 0 0 2436 2256 106 166 100 100 100 100 14807 15122 1.166 .858 .903 1 1 1 52 188 1 .98 80 2670 8030 79 87 147 155 0 8038 356 7682 .964 8420 8064 1.037 1.015 -.053 .021
5 791 980 182 289 609 691 912 1011 200 309 730 722 0 0 461 599 81 143 75 73 73 63 1300 1452 .881 1.135 .989 1 1 1 52 194 1 .92 80 2800 8020 78 86 160 168 0 1101 325 776 1.275 1136 811 .784 1.111 .35 .152
6 398 492 181 265 217 227 402 518 190 275 221 253 0 0 48 118 63 113 100 80 98 57 444 474 .956 1.046 1.145 1 1 1 52 255 1 .71 80 2960 8030 79 87 176 184 0 553 298 255 1.175 582 284 .851 1.286 .233 .363
7 429 1891 181 265 248 1626 425 2019 186 304 244 1754 0 0 121 532 103 467 90 96 60 87 1874 1998 .153 6.556 7.189 1 1 1 80 360 1 .89 100 3100 8030 78 88 189 199 0 2125 298 1827 7.367 2269 1971 .136 8.077 2.881 3.014
8 7051 15416 190 266 6861 15150 7513 16289 258 535 7323 16023 0 0 1489 3700 484 1502 100 100 100 100 22011 23346 .453 2.208 2.188 1 1 1 52 312 1 .98 90 3240 8020 77 86 203 212 0 17321 299 17022 2.481 18302 18003 .403 2.458 1.311 1.298
9 1824 2290 202 272 1622 2018 1820 2267 256 419 1618 1995 0 0 449 632 361 1061 100 96 98 44 3640 3613 .804 1.244 1.233 1 1 1 52 317 1 .94 90 3390 8020 77 86 218 227 0 2573 306 2267 1.398 2547 2242 .715 1.385 .483 .47
10 473 647 192 275 281 372 479 674 200 295 287 399 0 0 66 155 44 133 100 87 100 75 653 686 .755 1.324 1.39 1 1 1 32 152 1 .7 60 3540 8030 80 86 235 241 0 727 309 418 1.487 757 448 .672 1.562 .573 .643
11 248 343 179 261 69 82 194 293 185 276 15 32 0 0 230 204 41 112 26 28 21 9 151 47 .841 1.188 2.133 1 1 1 52 248 1 .63 80 3680 8030 79 87 248 256 0 385 293 92 1.335 329 36 .749 2.397 .417 1.261
12 1764 1198 175 246 1589 952 1772 1228 179 257 1597 982 0 0 434 324 55 102 100 100 100 98 2541 2579 1.669 .599 .615 1 1 1 52 301 1 .91 90 3820 8030 78 87 261 270 0 1346 276 1070 .673 1380 1103 1.486 .691 -.571 -.533
13 1038 1249 174 252 864 997 1102 1250 179 269 928 998 0 0 337 393 53 112 98 100 98 96 1861 1926 .867 1.154 1.075 1 1 1 80 326 1 .91 100 3980 8040 79 89 277 287 0 1403 283 1120 1.297 1404 1121 .771 1.208 .375 .273
14 415 3589 169 271 246 3318 420 3587 172 284 251 3316 0 0 73 784 34 98 100 100 100 100 3564 3567 .074 13.488 13.211 1 1 1 80 305 1 .91 100 4130 8040 79 89 292 302 0 4033 304 3728 15.155 4030 3726 .066 14.844 3.922 3.892
15 6016 2664 175 280 5841 2384 6467 2801 181 300 6292 2521 0 0 1712 616 47 148 100 100 100 98 8225 8813 2.45 .408 .401 1 1 1 80 316 1 .96 100 4270 8040 79 89 306 316 0 2993 315 2679 .459 3147 2833 2.181 .45 -1.125 -1.151
16 2071 2678 191 277 1880 2401 2048 2612 215 330 1857 2335 0 0 290 489 127 282 100 100 100 100 4281 4192 .783 1.277 1.257 1 1 1 52 278 1 .95 90 4400 8030 78 87 319 328 0 3009 311 2698 1.435 2935 2624 .697 1.413 .521 .499
17 464 441 183 271 281 170 455 436 199 300 272 165 0 0 101 103 107 225 98 31 70 0 451 437 1.653 .605 .607 1 1 1 80 384 1 .59 100 4560 8030 78 88 335 345 0 496 304 191 .68 490 185 1.471 .682 -.557 -.553
18 271 344 167 274 104 70 269 345 181 278 102 71 0 0 44 119 67 97 86 36 25 13 174 173 1.486 .673 .696 1 1 1 52 239 1 .26 80 4700 8030 79 87 350 358 0 387 308 79 .756 388 80 1.322 .782 -.403 -.355
19 2131 843 175 277 1956 566 2343 830 195 291 2168 553 0 0 701 216 97 127 100 98 100 91 2522 2721 3.456 .289 .255 1 1 1 120 461 1 .86 120 4860 8040 78 90 364 376 0 947 311 636 .325 933 621 3.076 .287 -1.621 -1.803
20 1509 990 175 269 1334 721 1535 1024 199 299 1360 755 0 0 231 205 121 162 100 100 100 98 2055 2115 1.85 .54 .555 1 1 1 52 249 1 .87 90 5000 8020 77 86 379 388 0 1112 302 810 .607 1151 848 1.647 .624 -.72 -.681

Total number of rows: 43008

Table truncated, full table size 9234 Kbytes.




Supplementary data files not provided
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