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Sample GSM97269 Query DataSets for GSM97269
Status Public on Feb 25, 2006
Title Ovarian Ca OV423_2
Sample type RNA
 
Channel 1
Source name CRD Reference
Organism Homo sapiens
Characteristics CRD Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ovarian Ca
Organism Homo sapiens
Characteristics Ovarian Ca
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/14962.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 17, 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 GPL2936
Series (1)
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 1638 1100 193 318 1445 782 1776 1130 199 348 1583 812 0 0 532 401 56 152 100 93 100 87 2227 2395 1.848 .541 .513 .532 .563 1.843 32 218 .523 .8 70 2540 16500 74 81 98 105 0 2102 608 1494 1.034 2159 1552 .967 .98 .048 -.029 .048
2 1061 812 181 332 880 480 1086 786 185 354 905 454 0 0 462 315 52 147 98 88 98 63 1360 1359 1.833 .545 .502 .497 .504 2.121 52 274 .571 .75 80 2690 16500 74 82 113 121 0 1552 634 917 1.042 1502 868 .959 .959 .06 -.061 .06
3 1375 648 190 329 1185 319 1506 639 203 344 1316 310 0 0 597 229 109 150 100 73 96 51 1504 1626 3.715 .269 .236 .275 .292 2.538 52 297 .228 .41 80 2830 16500 74 82 127 135 0 1238 629 610 .514 1221 592 1.944 .45 -.959 -1.152 -.959
4 708 602 202 363 506 239 747 598 227 388 545 235 0 0 238 193 141 186 90 56 81 28 745 780 2.117 .472 .431 .455 .416 2.774 32 173 .649 .4 60 3000 16510 76 82 145 151 0 1150 694 457 .903 1143 449 1.108 .824 -.148 -.279 -.148
5 4903 632 223 360 4680 272 5142 623 277 394 4919 263 0 0 1594 197 235 170 100 65 100 31 4952 5182 17.206 .058 .053 .061 .056 2.003 32 209 .046 .49 70 3130 16490 73 80 157 164 0 1208 688 520 .111 1190 503 9.004 .102 -3.171 -3.291 -3.171
6 1292 1253 207 366 1085 887 1402 731 234 409 1195 365 0 0 1229 3206 186 424 78 43 70 16 1972 1560 1.223 .818 .305 .656 .509 3.464 80 534 2.837 .89 110 3280 16490 71 82 170 181 0 2394 699 1695 1.562 1397 697 .64 .584 .644 -.777 .644
7 593 448 187 368 406 80 620 455 192 376 433 87 0 0 183 172 51 148 93 37 87 12 486 520 5.075 .197 .201 .391 .442 3.137 32 171 .232 .13 60 3450 16500 75 81 190 196 0 856 703 153 .377 869 166 2.656 .384 -1.409 -1.381 -1.409
8 1512 3181 202 365 1310 2816 753 1187 208 378 551 822 0 0 1923 5192 52 171 100 100 100 94 4126 1373 .465 2.15 1.492 1.626 1.46 1.826 52 332 2.733 .92 90 3590 16510 74 83 202 211 0 6078 697 5381 4.108 2268 1571 .243 2.851 2.038 1.511 2.038
9 11727 1270 205 383 11522 887 12645 1302 222 455 12440 919 0 0 5328 508 134 509 100 75 100 40 12409 13359 12.99 .077 .074 .072 .075 1.593 52 293 .075 .88 80 3740 16500 74 82 218 226 0 2427 732 1695 .147 2488 1756 6.798 .141 -2.765 -2.825 -2.765
10 1284 447 196 351 1088 96 1492 435 218 361 1296 84 0 0 534 137 104 133 93 43 90 9 1184 1380 11.333 .088 .065 .175 .163 3.155 32 224 .068 .24 70 3890 16500 74 81 233 240 0 854 671 183 .169 831 161 5.931 .124 -2.568 -3.013 -2.568
11 616 1130 199 355 417 775 622 1051 211 373 423 696 0 0 191 563 80 147 92 90 90 86 1192 1119 .538 1.859 1.645 1.65 1.854 2.381 52 284 2.568 .78 80 4040 16500 74 82 248 256 0 2159 678 1481 3.551 2008 1330 .282 3.144 1.828 1.653 1.828
12 3062 1106 211 400 2851 706 3237 1185 217 421 3026 785 0 0 1216 490 62 187 100 78 100 69 3557 3811 4.038 .248 .259 .232 .245 2.107 52 264 .24 .76 80 4190 16500 74 82 263 271 0 2113 764 1349 .473 2264 1500 2.113 .496 -1.079 -1.012 -1.079
13 1653 803 209 394 1444 409 1742 743 211 407 1533 349 0 0 479 322 60 166 100 76 100 51 1853 1882 3.531 .283 .228 .229 .276 2.543 52 275 .293 .62 80 4340 16500 74 82 278 286 0 1534 753 782 .541 1420 667 1.848 .435 -.886 -1.201 -.886
14 12651 1576 186 359 12465 1217 12631 1583 194 376 12445 1224 0 0 7377 860 52 160 100 85 100 78 13682 13669 10.242 .098 .098 .097 .102 1.561 80 440 .096 .91 110 4490 16490 71 82 291 302 0 3012 686 2326 .187 3025 2339 5.36 .188 -2.422 -2.412 -2.422
15 920 629 186 360 734 269 925 640 192 376 739 280 0 0 248 251 47 145 100 69 100 46 1003 1019 2.729 .366 .379 .384 .432 2.452 52 282 .441 .53 80 4640 16500 74 82 308 316 0 1202 688 514 .7 1223 535 1.428 .724 -.514 -.466 -.514
16 1483 1149 193 372 1290 777 1523 1145 199 396 1330 773 0 0 483 346 52 172 100 96 100 90 2067 2103 1.66 .602 .581 .571 .616 1.671 52 334 .627 .85 90 4800 16500 73 82 323 332 0 2196 711 1485 1.151 2188 1477 .869 1.111 .203 .151 .203
17 11576 3066 200 397 11376 2669 12397 3079 232 605 12197 2682 0 0 3145 1031 288 1912 100 73 100 13 14045 14879 4.262 .235 .22 .225 .24 1.432 52 348 .222 .92 90 4950 16500 73 82 338 347 0 5859 759 5100 .448 5884 5125 2.231 .42 -1.157 -1.251 -1.157
18 551 1025 213 458 338 567 565 988 271 808 352 530 0 0 146 383 410 2754 31 0 0 0 905 882 .596 1.678 1.506 1.461 1.615 2.334 32 165 5.503 .95 60 5100 16500 75 81 355 361 0 1959 875 1083 3.206 1888 1013 .312 2.877 1.681 1.525 1.681
19 4143 2710 197 373 3946 2337 4457 2542 204 386 4260 2169 0 0 1487 1160 53 168 100 98 100 98 6283 6429 1.688 .592 .509 .55 .58 1.547 52 313 .607 .92 90 5250 16510 74 83 368 377 0 5178 713 4466 1.132 4857 4145 .884 .973 .179 -.04 .179
20 1217 1074 192 374 1025 700 1303 1004 195 392 1111 630 0 0 395 427 48 164 98 90 98 78 1725 1741 1.464 .683 .567 .664 .741 1.934 52 274 .76 .82 80 5400 16500 74 82 384 392 0 2052 715 1338 1.305 1919 1204 .766 1.084 .384 .116 .384

Total number of rows: 24192

Table truncated, full table size 5456 Kbytes.




Supplementary data files not provided
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