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Sample GSM39930 Query DataSets for GSM39930
Status Public on Feb 21, 2005
Title Lymph node 0599
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Lymph node 0599
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/35858.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 1142 784 303 451 839 333 1242 781 308 460 939 330 0 0 393 290 67 108 94 73 92 71 1172 1269 2.52 .397 .351 .441 .427 2.424 52 332 .489 .76 90 1800 8600 51 60 51 60 0 585 337 249 .296 583 246 3.376 .262 -1.755 -1.931 -1.755
2 857 412 315 469 542 -57 910 422 327 477 595 -47 0 0 243 154 74 106 90 13 88 3 485 548 null null null .239 .166 4.934 52 253 -1 -1 80 1930 8600 52 60 65 73 0 307 350 -43 null 315 null null null null null null
3 2929 3216 300 460 2629 2756 3107 3512 306 466 2807 3052 0 0 1020 951 72 113 98 98 98 98 5385 5859 .954 1.048 1.087 1.08 1.035 1.757 80 358 1.031 .88 100 2080 8610 52 62 79 89 0 2400 343 2057 .782 2621 2278 1.278 .811 -.354 -.302 -.354
4 6834 12398 281 410 6553 11988 7315 13301 284 428 7034 12891 0 0 2935 5428 71 112 100 100 100 100 18541 19925 .547 1.829 1.833 1.866 1.871 1.986 52 300 1.945 .91 90 2220 8600 51 60 93 102 0 9252 306 8946 1.365 9926 9620 .732 1.368 .449 .452 .449
5 991 919 311 436 680 483 1027 973 314 447 716 537 0 0 283 291 79 115 96 84 92 80 1163 1253 1.408 .71 .75 .744 .745 1.719 52 256 .797 .79 80 2370 8600 52 60 109 117 0 686 325 360 .53 726 401 1.887 .56 -.916 -.837 -.916
6 1013 560 341 466 672 94 1105 591 349 480 764 125 0 0 315 172 71 114 90 51 90 17 766 889 7.149 .14 .164 .256 .235 2.877 52 235 .194 .41 80 2520 8600 52 60 124 132 0 418 348 70 .104 441 93 9.58 .122 -3.26 -3.034 -3.26
7 1741 4702 325 454 1416 4248 1950 5336 334 463 1625 4882 0 0 766 1818 71 108 93 97 90 97 5664 6507 .333 3 3.004 3.241 2.939 1.671 80 322 2.974 .91 100 2660 8610 52 62 137 147 0 3509 339 3170 2.239 3982 3643 .447 2.242 1.163 1.165 1.163
8 16523 36767 322 448 16201 36319 18379 43484 392 489 18057 43036 0 0 5251 14378 577 412 100 100 100 100 52520 61093 .446 2.242 2.383 2.075 2.306 1.728 80 406 2.389 .95 110 2810 8600 50 61 151 162 0 27438 334 27104 1.673 32451 32116 .598 1.779 .742 .831 .742
9 1294 1201 326 472 968 729 1487 1318 502 552 1161 846 0 0 564 552 829 571 68 71 6 18 1697 2007 1.328 .753 .729 .885 .83 2.581 32 195 .794 .79 70 2940 8610 53 60 166 173 0 896 352 544 .562 984 631 1.779 .544 -.831 -.879 -.831
10 456 429 299 408 157 21 397 376 325 417 98 -32 0 0 238 211 209 244 30 15 15 3 178 66 7.476 .134 null .985 .976 3.761 52 287 1.012 .62 80 3100 8600 52 60 182 190 -50 320 304 16 .1 281 null 10.018 null null -3.325
11 1969 3025 332 433 1637 2592 2062 3261 337 438 1730 2828 0 0 1336 1830 125 129 78 85 78 81 4229 4558 .632 1.583 1.635 1.492 1.506 2.339 80 380 1.572 .82 110 3250 8610 51 62 195 206 0 2257 323 1934 1.182 2434 2110 .846 1.22 .241 .287 .241
12 1684 1669 347 459 1337 1210 1277 1257 361 473 930 798 0 0 1745 1743 130 131 78 75 75 69 2547 1728 1.105 .905 .858 1.149 1.246 2.938 52 230 .899 .33 80 3380 8610 53 61 210 218 0 1246 343 903 .675 938 596 1.481 .64 -.566 -.643 -.566
13 875 734 333 435 542 299 922 797 353 439 589 362 0 0 482 321 150 154 81 68 68 56 841 951 1.813 .552 .615 .585 .741 3.904 32 202 .566 .62 70 3530 8620 54 61 225 232 0 548 325 223 .412 595 270 2.429 .459 -1.28 -1.125 -1.28
14 715 443 317 397 398 46 643 407 341 406 326 10 0 0 384 229 132 135 67 32 51 17 444 336 8.652 .116 .031 .576 .443 4.236 52 263 .409 .52 80 3690 8600 52 60 241 249 0 331 296 34 .086 304 7 11.594 .023 -3.535 -5.449 -3.535
15 11518 25034 312 391 11206 24643 12564 28332 318 412 12252 27941 0 0 7213 13729 77 120 91 100 90 100 35849 40193 .455 2.199 2.281 2.456 2.124 2.446 80 333 2.261 .89 100 3830 8610 52 62 254 264 0 18682 292 18390 1.641 21143 20851 .609 1.702 .715 .767 .715
16 2888 3209 317 426 2571 2783 3070 3404 334 439 2753 2978 0 0 1423 1185 106 123 92 100 88 98 5354 5731 .924 1.082 1.082 1.18 1.03 2.723 80 374 1.021 .85 100 3980 8610 52 62 269 279 0 2395 318 2077 .808 2540 2222 1.238 .807 -.308 -.309 -.308
17 625 456 272 378 353 78 717 478 286 407 445 100 0 0 258 182 88 129 81 46 75 15 431 545 4.526 .221 .225 .521 .438 2.8 32 150 .322 .29 60 4110 8600 53 59 284 290 0 340 282 58 .165 357 75 6.064 .168 -2.6 -2.576 -2.6
18 786 409 295 424 491 -15 792 407 382 410 497 -17 0 0 88 82 204 136 100 0 83 0 476 480 null null null .129 .123 1.555 12 92 -1 -1 50 4300 8600 53 58 303 308 0 305 316 -11 null 304 null null null null null null
19 2003 3043 292 401 1711 2642 2085 3130 300 414 1793 2729 0 0 562 974 78 109 100 100 100 100 4353 4522 .648 1.544 1.522 1.531 1.602 1.59 80 415 1.755 .86 110 4420 8600 50 61 312 323 0 2271 299 1972 1.152 2336 2037 .868 1.136 .205 .184 .205
20 701 417 321 400 380 17 723 419 326 407 402 19 0 0 215 135 70 96 90 26 84 9 397 421 22.353 .045 .047 .198 .209 3.276 52 223 .17 .25 80 4560 8590 51 59 328 336 -50 311 299 13 .033 313 14 29.953 .035 -4.825 -4.905

Total number of rows: 43008

Table truncated, full table size 9504 Kbytes.




Supplementary data files not provided
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