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Sample GSM39976 Query DataSets for GSM39976
Status Public on Feb 21, 2005
Title Liver 0032
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Liver 0032
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-07/18361.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 GPL1825
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
1 435 272 251 182 184 90 451 275 251 189 200 93 0 0 115 85 48 56 81 67 77 43 274 293 2.044 .489 .465 .567 .571 2.683 80 334 .534 .62 100 950 7880 99 109 66 76 0 296 198 98 .532 299 101 1.881 .505 -.911 -.984 -.911
2 425 752 258 193 167 559 348 358 263 200 90 165 0 0 199 743 50 59 62 65 45 53 726 255 .299 3.347 1.833 2.539 2.74 2.639 80 237 5.018 .81 100 1080 7880 99 109 79 89 -100 817 210 608 3.638 389 179 .275 1.993 .995 1.863
3 1806 952 259 203 1547 749 1927 964 269 207 1668 761 0 0 885 415 87 66 87 90 85 87 2296 2429 2.065 .484 .456 .607 .491 2.356 80 213 .46 .95 100 1220 7880 99 109 93 103 0 1035 221 814 .526 1048 827 1.9 .496 -.926 -1.012 -.926
4 379 264 265 208 114 56 327 237 273 205 62 29 0 0 140 110 88 71 41 30 26 22 170 91 2.036 .491 .468 .687 .684 3.249 80 212 .581 .61 100 1360 7880 99 109 107 117 0 287 226 61 .534 258 32 1.873 .508 -.905 -.976 -.905
5 750 379 240 186 510 193 778 365 240 190 538 179 0 0 253 110 48 58 90 90 87 77 703 717 2.642 .378 .333 .408 .344 2.407 80 256 .343 .78 100 1490 7880 99 109 120 130 0 412 202 210 .411 397 195 2.431 .362 -1.282 -1.467 -1.282
6 367 248 252 189 115 59 261 218 268 195 9 29 0 0 182 105 80 54 43 37 34 25 174 38 1.949 .513 3.222 .54 .49 2.457 32 116 .333 .62 70 1630 7880 100 107 135 142 -100 270 205 64 .558 237 32 1.793 3.502 1.808 -.843
7 709 415 275 210 434 205 770 396 294 220 495 186 0 0 282 175 95 73 80 81 75 63 639 681 2.117 .472 .376 .45 .452 1.88 80 252 .491 .76 100 1760 7880 99 109 147 157 0 451 228 223 .513 430 202 1.948 .408 -.962 -1.292 -.962
8 785 457 260 201 525 256 767 424 283 214 507 223 0 0 177 155 96 79 97 93 95 70 781 730 2.051 .488 .44 .451 .445 2.258 80 284 .446 .74 110 1920 7880 98 109 162 173 0 497 218 278 .53 461 242 1.887 .478 -.916 -1.065 -.916
9 612 317 259 195 353 122 616 278 271 204 357 83 0 0 211 143 70 61 87 59 78 34 475 440 2.893 .346 .232 .26 .302 2.98 32 171 .39 .61 70 2040 7830 95 102 176 183 0 345 212 133 .376 302 90 2.662 .253 -1.412 -1.984 -1.412
10 547 339 249 199 298 140 549 330 254 208 300 131 0 0 117 94 50 65 100 80 96 50 438 431 2.129 .47 .437 .492 .514 1.818 80 278 .47 .61 100 2180 7860 97 107 189 199 0 368 216 152 .511 359 142 1.958 .475 -.97 -1.075 -.97
11 1719 427 239 196 1480 231 1727 412 245 203 1488 216 0 0 286 94 48 60 100 98 100 92 1711 1704 6.407 .156 .145 .151 .148 1.44 52 224 .15 .81 90 2320 7840 95 104 203 212 0 464 213 251 .17 448 235 5.894 .158 -2.559 -2.664 -2.559
12 744 436 243 189 501 247 761 437 252 195 518 248 0 0 101 88 60 60 100 100 100 87 748 766 2.028 .493 .479 .469 .486 1.405 32 167 .5 .81 70 2430 7840 96 103 215 222 0 474 205 268 .536 475 270 1.866 .52 -.9 -.942 -.9
13 586 401 243 198 343 203 576 410 249 195 333 212 0 0 131 108 48 55 98 90 96 82 546 545 1.69 .592 .637 .537 .623 2.022 52 219 .654 .75 80 2590 7850 97 105 231 239 0 436 215 221 .643 446 230 1.554 .692 -.636 -.531 -.636
14 688 614 246 194 442 420 685 594 250 195 439 400 0 0 125 140 49 56 100 100 100 100 862 839 1.052 .95 .911 .938 .926 1.494 52 241 .963 .85 90 2720 7840 95 104 243 252 0 667 211 457 1.033 646 435 .968 .99 .047 -.014 .047
15 791 560 244 201 547 359 821 548 250 208 577 347 0 0 126 113 52 65 100 100 100 96 906 924 1.524 .656 .601 .641 .616 1.458 32 158 .662 .84 70 2850 7840 96 103 257 264 0 609 218 390 .713 596 377 1.402 .654 -.487 -.613 -.487
16 1351 731 249 202 1102 529 1378 717 255 210 1129 515 0 0 221 159 50 63 100 100 100 100 1631 1644 2.083 .48 .456 .469 .464 1.397 80 265 .471 .89 100 2980 7850 96 106 269 279 0 795 220 575 .522 779 560 1.917 .496 -.938 -1.012 -.938
17 739 516 237 207 502 309 732 521 241 212 495 314 0 0 133 152 43 58 100 94 100 88 811 809 1.625 .616 .634 .543 .584 1.865 52 186 .63 .83 80 3100 7840 96 104 282 290 0 561 225 336 .669 566 341 1.495 .69 -.58 -.536 -.58
18 587 320 234 193 353 127 596 326 234 197 362 133 0 0 113 86 51 61 100 76 98 55 480 495 2.78 .36 .367 .315 .415 2.234 80 302 .39 .67 100 3250 7840 95 105 296 306 0 348 210 138 .391 354 145 2.557 .399 -1.355 -1.324 -1.355
19 572 389 223 197 349 192 559 375 224 197 336 178 0 0 96 84 54 62 100 96 100 75 541 514 1.818 .55 .53 .508 .542 1.673 52 221 .587 .79 90 3380 7850 96 105 309 318 0 423 214 209 .598 408 193 1.672 .576 -.742 -.796 -.742
20 1051 597 224 205 827 392 1137 629 230 202 913 424 0 0 354 233 45 57 100 92 100 81 1219 1337 2.11 .474 .464 .422 .46 1.708 80 242 .507 .89 100 3520 7850 96 106 323 333 0 649 223 426 .515 684 461 1.941 .505 -.957 -.986 -.957

Total number of rows: 44160

Table truncated, full table size 9781 Kbytes.




Supplementary data files not provided
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