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Sample GSM39938 Query DataSets for GSM39938
Status Public on Feb 21, 2005
Title Buffycoat 3642
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Buffycoat 3642
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-04/27736.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
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 GPL1824
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
1 531 583 224 493 307 90 549 597 225 498 325 104 0 0 106 176 48 134 96 40 90 9 397 429 3.411 .293 .32 .38 .519 3.104 32 154 .96 .34 60 1450 8440 37 43 58 64 0 648 548 100 .326 663 116 3.07 .356 -1.618 -1.492 -1.618
2 398 563 226 464 172 99 401 568 227 472 175 104 0 0 98 131 50 118 86 44 80 15 271 279 1.737 .576 .594 .715 .804 3.473 52 281 2.392 .31 80 1600 8440 36 44 72 80 -50 626 516 110 .64 631 116 1.564 .66 -.599 -.645
3 2426 938 211 445 2215 493 2577 944 217 454 2366 499 0 0 608 230 50 135 98 93 98 82 2708 2865 4.493 .223 .211 .211 .234 1.501 80 349 .204 .82 100 1740 8450 36 46 85 95 0 1042 494 548 .247 1049 554 4.044 .234 -2.016 -2.093 -2.016
4 7119 8502 227 478 6892 8024 7588 8125 232 491 7361 7647 0 0 3653 4328 48 125 100 100 98 98 14916 15008 .859 1.164 1.039 1.215 1.188 2.242 52 253 1.176 .96 80 1890 8450 37 45 101 109 0 9447 531 8916 1.294 9028 8497 .773 1.154 .371 .207 .371
5 833 5431 218 470 615 4961 838 5460 219 484 620 4990 0 0 162 845 45 137 100 100 100 100 5576 5610 .124 8.067 8.048 8.243 7.847 1.306 32 219 8.443 .91 70 2040 8440 36 43 116 123 0 6034 522 5512 8.963 6067 5544 .112 8.943 3.164 3.161 3.164
6 444 671 206 451 238 220 421 659 210 464 215 208 0 0 165 182 47 128 80 67 75 42 458 423 1.082 .924 .967 1.243 .909 3.738 52 270 1.41 .57 80 2180 8430 35 43 130 138 -50 746 501 244 1.027 732 231 .974 1.075 .104 .039
7 942 59237 202 398 740 58839 956 62511 204 409 754 62113 0 11 186 10204 51 128 100 100 98 100 59579 62867 .013 79.512 82.378 75.33 77.766 1.241 52 254 81.58 .95 80 2330 8450 37 45 145 153 0 65819 442 65377 88.347 69457 69014 .011 91.531 6.465 6.516 6.465
8 12757 19152 214 417 12543 18735 13586 20726 216 422 13372 20309 0 0 3409 5234 47 127 100 100 100 100 31278 33681 .669 1.494 1.519 1.519 1.49 1.423 52 313 1.524 .97 90 2480 8450 36 45 159 168 0 21280 463 20817 1.66 23029 22566 .603 1.688 .731 .755 .731
9 1335 2701 236 456 1099 2245 1359 2665 239 470 1123 2209 0 0 287 814 53 145 100 100 100 100 3344 3332 .49 2.043 1.967 1.968 1.982 1.336 32 207 2.198 .92 70 2630 8450 37 44 175 182 0 3001 507 2494 2.27 2961 2454 .441 2.186 1.183 1.128 1.183
10 272 489 206 372 66 117 248 451 209 392 42 79 0 0 87 170 48 130 48 42 32 19 183 121 .564 1.773 1.881 1.727 1.96 2.865 52 249 3.77 .44 80 2760 8430 35 43 188 196 -50 543 413 130 1.97 501 88 .508 2.09 1.063 .978
11 1914 1022 205 383 1709 639 1908 998 216 399 1703 615 0 0 307 251 109 160 100 99 100 89 2348 2318 2.674 .374 .361 .35 .367 1.529 120 560 .386 .86 130 2920 8450 34 47 201 214 0 1136 426 710 .415 1109 683 2.407 .401 -1.267 -1.317 -1.267
12 1262 838 205 395 1057 443 1308 795 207 402 1103 400 0 0 462 285 43 108 100 87 100 75 1500 1503 2.386 .419 .363 .385 .429 1.979 32 150 .426 .73 60 3060 8440 37 43 219 225 0 931 439 492 .466 883 444 2.147 .403 -1.103 -1.311 -1.103
13 1007 824 193 353 814 471 1082 803 203 371 889 450 0 0 428 357 78 144 96 78 90 62 1285 1339 1.728 .579 .506 .514 .584 2.018 32 160 .57 .72 60 3200 8450 38 44 233 239 0 916 392 523 .643 892 500 1.555 .562 -.637 -.83 -.637
14 246 356 154 274 92 82 234 336 169 294 80 62 0 0 93 138 66 121 59 30 30 11 174 142 1.122 .891 .775 1.403 1.323 3.388 52 288 2.265 .45 80 3340 8430 35 43 246 254 -50 396 304 91 .99 373 69 1.01 .861 -.216 -.014
15 5557 3522 137 228 5420 3294 6213 3572 143 235 6076 3344 0 0 2165 1138 34 89 100 100 98 100 8714 9420 1.645 .608 .55 .666 .597 2.047 52 256 .579 .94 80 3500 8440 36 44 262 270 0 3913 253 3660 .675 3969 3716 1.481 .612 -.566 -.71 -.566
16 2606 967 139 218 2467 749 2872 1014 153 223 2733 796 0 0 932 258 97 76 100 100 100 100 3216 3529 3.294 .304 .291 .314 .312 1.734 32 191 .26 .83 70 3630 8440 36 43 275 282 0 1074 242 832 .337 1127 884 2.964 .324 -1.568 -1.628 -1.568
17 233 325 169 287 64 38 236 310 178 304 67 23 0 0 75 122 87 123 42 23 7 5 102 90 1.684 .594 .343 1.046 1.439 3.82 52 267 3.92 .33 80 3780 8430 35 43 290 298 -50 361 319 42 .66 344 26 1.516 .381 -1.391 -.6
18 320 390 208 409 112 -19 326 388 209 420 118 -21 0 0 89 109 46 121 73 7 57 1 93 97 null null null .798 .647 4.81 52 246 -1 -1 80 3930 8430 35 43 305 313 -50 433 454 -21 null 431 null null null null null
19 1116 990 218 422 898 568 1129 985 221 436 911 563 0 0 285 319 45 111 100 88 100 88 1466 1474 1.581 .633 .618 .567 .637 2.136 80 369 .66 .76 100 4080 8440 35 45 319 329 0 1100 469 631 .703 1094 626 1.423 .687 -.509 -.542 -.509
20 304 405 217 435 87 -30 298 446 226 442 81 11 0 0 125 153 77 105 51 17 26 1 57 92 null null .136 1.361 1.324 3.732 52 253 10.326 .08 80 4220 8430 35 43 334 342 -50 450 483 -33 null 496 12 null .151 -2.728 null

Total number of rows: 43008

Table truncated, full table size 9291 Kbytes.




Supplementary data files not provided
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