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Sample GSM6292 Query DataSets for GSM6292
Status Public on Apr 15, 2004
Title AML 105
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 105
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=710640LaserPower=4.014.07
Lot batch = shcz089
 
Submission date May 07, 2003
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 GPL318
Series (1)
GSE425 Acute myeloid leukemia study

Data table header descriptions
ID_REF
CH1D_MEDIAN Median spot pixel intensity at Channel 1 with the median-background subtracted (CH1I_MEDIAN - CH1B_MEDIAN)
CH1I_MEDIAN Median spot pixel intensity at Channel 1
CH1_PER_SAT Percentage of spot pixels at Channel 1 that are saturated
CH1I_SD Standard deviation of the spot intensity at Channel 1
CH1B_MEAN Mean spot background in Channel 1
CH1B_MEDIAN Median spot background intensity in Channel 1
CH1B_SD Standard deviation of the spot background intensity in Channel 1
CH1D_MEAN Mean Channel 1 intensity with the median-background subtracted (CH1I_MEAN - CH1B_MEDIAN)
CH2I_MEAN Mean spot pixel intensity at Channel 2
CH2D_MEAN Mean spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEAN - CH2B_MEDIAN)
CH2D_MEDIAN Median spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEDIAN - CH2B_MEDIAN)
CH2I_MEDIAN Median spot pixel intensity at Channel 2
CH2_PER_SAT Percentage of spot pixels at Channel 2 that are saturated
CH2I_SD Standard deviation of the spot pixel intensity at at Channel 2
CH2B_MEAN Mean spot background intensity in Channel 2
CH2B_MEDIAN Median spot background intensity in Channel 2
CH2B_SD Standard deviation of the spot background intensity in Channel 2
CH2BN_MEDIAN Normalized value of median Channel 2 background (CH2B_MEDIAN/Normalization factor)
CH2DN_MEAN Normalized value of mean Channel 2 intensity with normalized background subtracted (CH2IN_MEAN - CH2BN)
CH2IN_MEAN Normalized value of mean Channel 2 intensity (CH2I_MEAN/Normalization factor)
CH2DN_MEDIAN Normalized value of median Channel 2 intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN)
CH2IN_MEDIAN Normalized value of median Channel 2 intensity (CH2_MEDIAN/Normalization factor)
CORR Coefficient of determination for the current regression value
DIAMETER Diameter in µm of the spot indicator
FLAG Type of flag associated with a spot (default=0)
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the medians of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEDIAN)]
PIX_RAT2_MEAN Geometric mean of the pixel-by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PIX_RAT2_MEDIAN Median of pixel by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PERGTBCH1I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 1
PERGTBCH1I_2SD
PERGTBCH2I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 2
PERGTBCH2I_2SD Percentage of spot pixels with intensities more than two standard deviations above the background pixel intensity, at Channel 1
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
RAT1N_MEAN Ratio of the means of Channel 1 intensity to normalized Channel 2 intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized
RAT2_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 2/Channel 1 ratio, (CH2I_MEAN - CH2B_MEDIAN)/(CH1_MEAN - CH1B_MEDIAN) or Red/Green ratio
RAT2_MEDIAN Ratio of the median intensities of each spot for each wavelength, with the median background subtracted
RAT2_SD Standard deviation of pixel intensity ratios
RAT2N_MEAN Channel 2/Channel 1 ratio normalized, RAT2N_MEAN/Normalization factor or Red/Green mean ratio normalized
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2N_MEDIAN/Normalization factor or Red/Green median ratio normalized
REGR Regression ratio
SUM_MEAN Sum of the arithmetic mean intensities for each wavelength, with the median background subtracted (CH1D_MEAN + CH2D_MEAN)
SUM_MEDIAN Sum of the median intensities for each wavelength, with the median-background subtracted (CH1D_MEDIAN + CH2D_MEDIAN)
TOT_BPIX Total number of background pixels
TOT_SPIX Total number of signal (spot) pixels
X_COORD X-coordinate in µm of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
Y_COORD Y-coordinate in µm of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize)
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize)
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize)
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize)
UNF_VALUE aka LOG_RAT2N_MEAN, or Log (base 2) of the ratio of the mean of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEAN)]

Data table
ID_REF CH1D_MEDIAN CH1I_MEDIAN CH1_PER_SAT CH1I_SD CH1B_MEAN CH1B_MEDIAN CH1B_SD CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2D_MEDIAN CH2I_MEDIAN CH2_PER_SAT CH2I_SD CH2B_MEAN CH2B_MEDIAN CH2B_SD CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CH2DN_MEDIAN CH2IN_MEDIAN CORR DIAMETER FLAG VALUE LOG_RAT2N_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH1I_2SD PERGTBCH2I_1SD PERGTBCH2I_2SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2_MEDIAN RAT2_SD RAT2N_MEAN RAT2N_MEDIAN REGR SUM_MEAN SUM_MEDIAN TOT_BPIX TOT_SPIX X_COORD Y_COORD TOP BOT LEFT RIGHT UNF_VALUE
1 355 478 0 183 125 123 25 333 438 309 317 446 0 124 134 129 43 208 498 706 511 719 .84 100 0 .582 .526 1.015 .905 93 91 98 96 1.078 .668 .928 .893 1.947 1.497 1.44 .859 642 672 441 80 2620 7800 35 45 21 31 .582
2 1748 1870 0 784 124 122 26 1758 376 233 220 363 0 162 143 143 46 231 376 606 355 585 .77 80 0 -2.226 -2.3 .123 .13 100 100 84 76 7.545 4.678 .133 .126 1.963 .214 .203 .118 1991 1968 244 52 2770 7800 36 44 37 45 -2.226
3 931 1054 0 376 126 123 27 956 647 509 519 657 0 218 140 138 44 223 821 1044 837 1060 .91 80 0 -.22 -.153 .508 .508 100 100 98 96 1.878 1.164 .532 .557 1.521 .859 .899 .517 1465 1450 257 52 2910 7800 36 44 51 59 -.22
4 440 563 0 184 126 123 26 439 281 150 161 292 0 80 136 131 45 211 242 453 260 471 .76 80 0 -.86 -.761 .304 .343 100 100 88 76 2.927 1.815 .342 .366 1.936 .551 .59 .315 589 601 254 52 3050 7800 36 44 65 73 -.86
5 299 420 0 258 125 121 29 372 319 189 168 298 0 146 137 130 48 210 305 515 271 481 .87 100 0 -.287 -.142 .487 .529 97 93 82 67 1.968 1.22 .508 .562 2.099 .819 .906 .513 561 467 357 80 3200 7800 35 45 79 89 -.287
6 434 557 0 201 126 123 28 450 315 185 175 305 0 105 136 130 46 210 298 508 282 492 .79 80 0 -.593 -.621 .357 .404 100 100 90 78 2.432 1.508 .411 .403 2.141 .663 .65 .406 635 609 242 52 3340 7800 36 44 94 102 -.593
7 565 691 0 258 128 126 29 580 724 593 586 717 0 259 136 131 48 211 956 1168 945 1156 .92 90 0 .722 .742 .933 1.033 100 100 96 96 .978 .606 1.022 1.037 2.147 1.649 1.673 1.017 1173 1151 312 52 3490 7810 36 45 108 117 .722
8 358 480 0 166 201 122 919 352 278 143 114 249 0 107 156 135 231 218 231 448 184 402 .96 90 0 -.61 -.961 .342 .37 0 0 19 1 2.462 1.526 .406 .318 2.194 .655 .514 .254 495 472 289 52 3640 7800 35 44 123 132 -.61
9 347 466 0 199 123 119 27 331 300 167 150 283 0 117 137 133 45 215 269 484 242 456 .82 80 0 -.297 -.52 .475 .539 90 86 78 73 1.982 1.229 .505 .432 2.128 .814 .697 .506 498 497 250 52 3770 7800 36 44 137 145 -.297
10 408 531 0 117 129 123 39 413 302 173 177 306 0 76 134 129 43 208 279 487 285 494 .75 90 0 -.566 -.515 .393 .407 100 100 94 86 2.387 1.48 .419 .434 1.875 .676 .7 .367 586 585 299 52 3930 7800 35 44 152 161 -.566
11 763 885 0 654 127 122 39 889 428 298 248 378 0 244 138 130 48 210 481 690 400 610 .87 80 0 -.887 -.932 .415 .328 88 86 86 82 2.983 1.85 .335 .325 3.464 .541 .524 .319 1187 1011 270 52 4060 7800 36 44 166 174 -.887
12 753 873 0 737 121 120 26 954 856 726 583 713 0 514 135 130 46 210 1171 1381 940 1150 .89 90 0 .296 .321 .787 .791 100 100 100 96 1.314 .815 .761 .774 1.933 1.227 1.249 .709 1680 1336 306 52 4230 7800 35 44 182 191 .296
13 336 460 0 321 124 124 27 404 594 463 380 511 0 334 136 131 47 211 747 958 613 824 .86 80 0 .886 .867 1.195 1.142 88 86 90 88 .873 .541 1.146 1.131 2.026 1.848 1.824 1.112 867 716 257 52 4360 7800 36 44 196 204 .886
14 251 375 0 142 124 124 27 248 258 128 115 245 0 75 132 130 43 210 206 416 185 395 .7 70 0 -.265 -.436 .537 .488 96 90 90 71 1.938 1.201 .516 .458 2.825 .832 .739 .518 376 366 199 32 4510 7810 37 44 211 218 -.265
15 304 429 0 188 126 125 28 304 4530 4400 3995 4125 0 2422 135 130 47 210 7097 7306 6444 6653 .94 100 0 4.545 4.406 15.502 14.95 91 86 100 100 .069 .043 14.474 13.141 1.678 23.345 21.196 14.772 4704 4299 386 80 4660 7800 35 45 225 235 4.545
16 2891 3015 0 1298 127 124 32 2661 3667 3529 3849 3987 0 1427 140 138 51 223 5692 5915 6208 6431 .97 90 0 1.097 1.103 1.486 1.341 100 98 100 100 .754 .468 1.326 1.331 1.648 2.139 2.147 1.257 6190 6740 309 52 4800 7790 34 43 239 248 1.097
17 655 780 0 298 126 125 34 593 1853 1724 1623 1752 0 821 134 129 50 208 2781 2989 2618 2826 .91 100 0 2.229 1.999 3.295 2.907 96 93 100 100 .344 .213 2.907 2.478 1.836 4.689 3.997 3.056 2317 2278 374 80 4950 7800 35 45 254 264 2.229
18 352 478 0 192 128 126 28 327 232 102 81 211 0 107 132 130 39 210 165 374 131 340 .55 60 0 -.991 -1.43 .371 .326 93 90 71 50 3.206 1.988 .312 .23 2.881 .503 .371 .285 429 433 152 32 5090 7800 37 43 270 276 -.991
19 637 758 0 431 123 121 27 719 471 340 266 397 0 231 134 131 43 211 548 760 429 640 .9 80 0 -.391 -.57 .459 .45 100 100 96 88 2.115 1.311 .473 .418 1.955 .763 .674 .468 1059 903 271 52 5240 7790 35 43 284 292 -.391
20 730 853 0 325 129 123 39 691 571 436 459 594 0 238 140 135 52 218 703 921 740 958 .91 70 0 .025 .02 .57 .605 100 100 93 90 1.585 .983 .631 .629 1.688 1.018 1.014 .614 1127 1189 211 32 5370 7790 35 42 297 304 .025

Total number of rows: 43008

Table truncated, full table size 9357 Kbytes.




Supplementary data files not provided
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