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Sample GSM39897 Query DataSets for GSM39897
Status Public on Feb 21, 2005
Title Ovary 0538
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Ovary 0538
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26268.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

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
1 353 857 231 569 122 288 355 867 225 527 124 298 0 0 110 217 95 202 58 63 27 35 410 422 .424 2.361 2.403 2.311 2.313 1.81 80 397 2.531 .64 100 1430 7950 14 24 14 24 -100 697 463 234 1.919 705 242 .521 1.954 .966 .941
2 279 434 219 506 60 -72 271 436 224 482 52 -70 0 0 61 108 95 160 23 3 2 1 -12 -18 null null null 1.134 1.314 6.111 80 358 4.486 .23 100 1580 7950 14 24 29 39 -100 353 411 -59 null 354 null null null null null
3 1423 1396 211 465 1212 931 1482 1409 216 447 1271 944 0 0 356 340 73 118 100 100 100 98 2143 2215 1.302 .768 .743 .765 .779 1.528 52 301 .745 .86 90 1740 7950 14 23 45 54 0 1135 378 757 .625 1146 767 1.601 .604 -.679 -.728 -.679
4 4804 7683 212 449 4592 7234 5390 7711 216 444 5178 7262 0 0 1831 2107 53 83 100 100 100 100 11826 12440 .635 1.575 1.402 1.746 1.546 1.92 52 301 1.555 .89 90 1880 7950 14 23 59 68 0 6246 365 5881 1.281 6269 5904 .781 1.14 .357 .189 .357
5 568 741 210 430 358 311 609 769 212 426 399 339 0 0 169 147 51 74 90 90 90 86 669 738 1.151 .869 .85 .991 .87 2.857 52 243 .88 .73 80 2030 7950 15 23 75 83 0 602 350 253 .706 625 276 1.416 .691 -.502 -.534 -.502
6 296 429 206 411 90 18 290 431 209 411 84 20 0 0 89 73 44 69 67 23 48 5 108 104 5 .2 .238 .616 .724 3.203 80 342 .294 .08 100 2160 7950 14 24 87 97 -50 349 334 15 .163 350 16 6.15 .194 -2.369 -2.621
7 597 445 212 413 385 32 634 453 217 417 422 40 0 0 167 81 45 69 94 30 90 9 417 462 12.031 .083 .095 .182 .169 2.625 52 276 .106 .22 90 2320 7960 15 24 103 112 0 362 336 26 .068 368 33 14.798 .077 -3.887 -3.698 -3.887
8 2394 10271 205 404 2189 9867 2797 11032 210 410 2592 10628 0 0 1356 4582 41 61 92 100 91 100 12056 13220 .222 4.508 4.1 5.257 4.337 2.234 80 343 4.685 .84 100 2460 7940 13 23 117 127 0 8350 328 8022 3.665 8969 8641 .273 3.334 1.874 1.737 1.874
9 994 1227 200 376 794 851 1086 1294 206 386 886 918 0 0 283 283 40 75 100 100 100 94 1645 1804 .933 1.072 1.036 1.067 1.115 1.893 52 268 1.076 .87 80 2610 7950 15 23 133 141 0 998 306 692 .871 1052 746 1.148 .842 -.199 -.247 -.199
10 369 543 197 377 172 166 391 559 200 378 194 182 0 0 95 109 40 68 88 86 78 73 338 376 1.036 .965 .938 1.021 .951 2.366 52 234 1.23 .56 80 2750 7950 15 23 147 155 0 441 307 135 .785 454 148 1.274 .763 -.35 -.391 -.35
11 1106 1242 191 362 915 880 1089 1226 192 363 898 864 0 0 423 325 39 64 100 96 98 96 1795 1762 1.04 .962 .962 1.114 .99 1.989 52 288 .911 .84 90 2900 7950 14 23 161 170 0 1010 294 715 .782 997 702 1.279 .782 -.355 -.354 -.355
12 1106 1383 194 332 912 1051 1176 1476 195 333 982 1144 0 0 345 359 39 59 98 96 96 96 1963 2126 .868 1.152 1.165 1.174 1.077 1.556 52 234 1.128 .9 80 3040 7950 15 23 176 184 0 1124 270 854 .937 1200 930 1.067 .947 -.094 -.078 -.094
13 3472 871 189 306 3283 565 814 741 193 311 625 435 0 0 9934 767 38 57 100 90 100 88 3848 1060 5.811 .172 .696 .533 .639 3.754 52 252 .027 .31 80 3190 7950 15 23 191 199 -100 708 249 459 .14 602 354 7.147 .566 -.821 -2.837
14 306 372 196 339 110 33 292 362 197 344 96 23 0 0 111 81 39 61 63 38 51 10 143 119 3.333 .3 .24 .576 .5 3.787 80 316 .567 .29 100 3330 7950 14 24 204 214 -50 302 276 27 .244 294 19 4.1 .195 -2.36 -2.036
15 3322 6973 202 365 3120 6608 3811 7619 211 379 3609 7254 0 0 1751 2875 69 83 98 100 98 100 9728 10863 .472 2.118 2.01 2.39 1.95 1.802 52 268 1.966 .92 90 3470 7940 13 22 218 227 0 5669 297 5372 1.722 6194 5898 .581 1.634 .784 .709 .784
16 1482 2447 204 378 1278 2069 1691 2701 211 383 1487 2323 0 0 664 863 63 79 97 97 93 97 3347 3810 .618 1.619 1.562 1.816 1.601 1.871 80 333 1.566 .91 100 3620 7940 13 23 233 243 0 1989 307 1682 1.316 2196 1889 .76 1.27 .396 .345 .396
17 240 319 192 354 48 -35 240 322 200 358 48 -32 0 0 61 69 42 56 55 6 23 1 13 16 null null null 1.324 1.096 5.468 80 287 .44 .11 100 3770 7950 14 24 248 258 -50 259 288 -28 null 262 null null null null null
18 251 320 191 338 60 -18 249 325 198 347 58 -13 0 0 64 74 45 56 61 16 30 3 42 45 null null null .862 .907 5.937 80 320 .583 .17 100 3910 7950 14 24 262 272 -50 260 275 -15 null 264 null null null null null
19 677 853 188 328 489 525 666 846 194 334 478 518 0 0 283 310 46 58 93 93 90 93 1014 996 .931 1.074 1.084 1.075 1.007 1.648 32 175 1.158 .79 70 4060 7960 16 23 278 285 0 693 267 427 .873 688 421 1.146 .881 -.196 -.183 -.196
20 247 318 188 323 59 -5 250 324 193 325 62 1 0 0 79 72 41 55 56 17 43 5 54 63 null null .016 .503 .533 4.225 80 356 1.716 .06 100 4200 7940 13 23 291 301 -50 259 263 -4 null 263 1 null .013 -6.253 null

Total number of rows: 43008

Table truncated, full table size 9403 Kbytes.




Supplementary data files not provided
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