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Sample GSM90061 Query DataSets for GSM90061
Status Public on Dec 30, 2005
Title PN318_1
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PN318_1
Organism Homo sapiens
Characteristics PN318_1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, Non-tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24164.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 Dec 29, 2005
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 GPL3044
Series (1)
GSE3933 Prostate Cancer

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
1 616 285 381 100 235 185 592 291 389 106 211 191 0 0 145 82 88 34 88 98 59 92 420 402 1.27 .787 .905 .815 .852 1.905 52 359 .586 .74 90 1750 8490 84 93 86 95 0 169 59 109 .466 172 113 2.147 .536 -1.102 -.901
2 504 228 381 102 123 126 501 237 394 107 120 135 0 0 69 57 87 36 65 90 28 81 249 255 .976 1.024 1.125 1.02 1.085 2.086 32 197 .623 .53 70 1900 8470 83 90 102 109 0 135 60 75 .606 140 80 1.65 .666 -.722 -.587
3 1086 2329 379 101 707 2228 1154 2622 401 125 775 2521 0 0 352 1109 129 143 93 100 86 96 2935 3296 .317 3.151 3.253 3.102 2.875 1.832 80 478 3.227 .91 110 2030 8480 82 93 113 124 0 1378 60 1318 1.865 1551 1492 .536 1.925 .899 .945
4 2301 9639 377 104 1924 9535 2269 8297 391 135 1892 8193 0 0 1324 7045 127 168 90 100 80 96 11459 10085 .202 4.956 4.33 5.021 4.927 2.404 52 334 5.663 .9 90 2200 8480 83 92 131 140 0 5704 62 5642 2.932 4909 4848 .341 2.562 1.552 1.357
5 652 1085 365 99 287 986 665 1181 373 109 300 1082 0 0 171 529 63 42 86 100 76 100 1273 1382 .291 3.436 3.607 3.519 3.516 1.74 52 321 3.607 .85 90 2350 8490 84 93 146 155 0 642 59 583 2.033 699 640 .492 2.134 1.024 1.094
6 496 279 364 100 132 179 508 275 370 112 144 175 0 0 81 77 69 46 75 100 56 87 311 319 .737 1.356 1.215 1.437 1.192 2.209 32 216 1.037 .58 70 2510 8480 84 91 163 170 0 165 59 106 .802 163 104 1.246 .719 -.318 -.476
7 755 366 349 93 406 273 770 360 354 97 421 267 0 0 207 101 58 29 94 100 94 98 679 688 1.487 .672 .634 .707 .614 1.854 52 296 .58 .8 90 2640 8470 82 91 175 184 0 217 55 162 .398 213 158 2.513 .375 -1.33 -1.414
8 2256 4773 350 93 1906 4680 2078 4839 350 96 1728 4746 0 0 1341 2864 51 25 96 100 92 100 6586 6474 .407 2.455 2.747 2.721 2.342 2.314 80 380 2.503 .9 100 2780 8480 83 93 189 199 0 2824 55 2769 1.453 2863 2808 .688 1.625 .539 .701
9 877 1406 344 93 533 1313 977 1526 347 97 633 1433 0 0 326 837 51 27 92 100 84 100 1846 2066 .406 2.463 2.264 2.53 2.451 1.864 52 223 2.638 .91 80 2930 8490 85 93 205 213 0 832 55 777 1.458 903 848 .686 1.34 .544 .422
10 425 538 340 93 85 445 426 349 347 107 86 256 0 0 84 415 79 82 51 76 15 61 530 342 .191 5.235 2.977 4.08 4.577 3.256 80 357 5.758 .62 100 3070 8470 82 92 218 228 -50 318 55 263 3.098 207 151 .323 1.761 1.631 .817
11 1557 2046 342 100 1215 1946 1652 2209 345 112 1310 2109 0 0 627 851 76 80 96 100 92 100 3161 3419 .624 1.602 1.61 1.778 1.552 1.709 80 433 1.522 .94 110 3220 8480 82 93 232 243 0 1211 59 1151 .948 1307 1248 1.055 .953 -.077 -.07
12 1032 994 338 93 694 901 1038 969 339 98 700 876 0 0 492 568 51 43 94 100 88 98 1595 1576 .77 1.298 1.251 1.512 1.263 2.411 52 274 1.276 .9 90 3370 8470 82 91 248 257 0 588 55 533 .768 573 518 1.302 .74 -.38 -.433
13 756 801 342 94 414 707 747 783 345 97 405 689 0 0 254 437 52 28 97 98 92 96 1121 1094 .586 1.708 1.701 1.579 1.622 2.231 80 326 1.821 .88 100 3510 8480 83 93 262 272 0 474 56 418 1.01 463 408 .99 1.007 .015 .01
14 486 309 349 102 137 207 492 311 348 132 143 209 0 0 97 62 56 282 76 13 55 0 344 352 .662 1.511 1.462 1.606 1.376 2.084 52 262 .989 .55 80 3660 8480 84 92 278 286 0 183 60 122 .894 184 124 1.119 .865 -.162 -.21
15 2317 4216 331 95 1986 4121 1990 4127 331 117 1659 4032 0 0 1466 2871 53 222 96 100 92 93 6107 5691 .482 2.075 2.43 2.137 1.981 2.006 80 429 2.23 .91 110 3810 8480 82 93 291 302 0 2495 56 2438 1.228 2442 2386 .814 1.438 .296 .524
16 1274 2533 323 98 951 2435 1328 2579 323 101 1005 2481 0 0 539 1350 49 28 100 100 96 100 3386 3486 .391 2.56 2.469 2.716 2.628 1.648 80 377 2.728 .93 100 3950 8480 83 93 306 316 0 1499 58 1441 1.515 1526 1468 .66 1.461 .599 .547
17 466 521 325 95 141 426 446 543 325 97 121 448 0 0 119 161 47 25 88 100 67 100 567 569 .331 3.021 3.702 3.347 3.326 1.992 52 312 3.081 .62 90 4100 8470 82 91 321 330 0 308 56 252 1.788 321 265 .559 2.191 .838 1.131
18 439 208 315 94 124 114 434 205 318 101 119 111 0 0 82 50 48 50 82 92 65 63 238 230 1.088 .919 .933 .976 .874 2.544 52 265 .716 .43 90 4240 8480 83 92 335 344 0 123 56 67 .544 121 66 1.838 .552 -.878 -.857
19 847 1549 312 97 535 1452 845 1381 320 102 533 1284 0 0 251 796 51 43 98 100 96 98 1987 1817 .368 2.714 2.409 2.473 2.524 1.593 80 411 2.863 .92 110 4380 8470 81 92 348 359 0 917 57 859 1.606 817 760 .623 1.425 .683 .511
20 474 306 322 97 152 209 472 296 326 113 150 199 0 0 72 64 59 105 96 98 63 40 361 349 .727 1.375 1.327 1.481 1.426 1.715 52 263 1.209 .69 80 4530 8480 84 92 365 373 0 181 57 124 .814 175 118 1.229 .785 -.298 -.349

Total number of rows: 43008

Table truncated, full table size 9361 Kbytes.




Supplementary data files not provided
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