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Sample GSM6297 Query DataSets for GSM6297
Status Public on Apr 15, 2004
Title AML 66
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 66
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix Pro
Software version: 3.0.6.81
Scanning parameters: PMTVolts=780630LaserPower=3.584.73
Lot batch = shcz106
 
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
1 526 730 0 267 210 204 49 506 503 237 203 469 0 211 279 266 101 467 416 882 356 823 .65 60 0 -.283 -.563 .402 .528 93 93 65 50 2.135 1.217 .468 .386 2.701 .822 .677 .574 743 729 154 32 1670 8020 27 33 20 26 -.283
2 1710 1917 0 964 209 207 45 1681 961 678 599 882 0 471 287 283 113 496 1189 1686 1051 1547 .91 60 0 -.499 -.702 .369 .449 96 96 87 78 2.479 1.413 .403 .35 1.643 .708 .615 .405 2359 2309 170 32 1810 8020 27 33 34 40 -.499
3 3946 4151 0 2288 217 205 66 4132 1683 1406 1424 1701 0 819 285 277 102 486 2467 2953 2498 2984 .96 70 0 -.744 -.659 .318 .339 100 100 96 87 2.939 1.675 .34 .361 1.99 .597 .633 .337 5538 5370 232 32 1960 8020 26 33 48 55 -.744
4 488 686 0 231 204 198 50 489 823 533 505 795 0 317 297 290 110 509 935 1444 886 1395 .83 60 0 .935 .86 .996 .997 100 93 90 81 .917 .523 1.09 1.035 1.865 1.912 1.816 1.258 1022 993 170 32 2100 8020 27 33 63 69 .935
5 1332 1563 0 574 272 231 166 1339 1316 1013 1149 1452 0 408 313 303 118 532 1777 2309 2016 2547 .91 50 0 .408 .598 .789 .773 100 91 100 100 1.322 .753 .757 .863 1.512 1.327 1.513 .746 2352 2481 104 12 2240 8020 27 32 77 82 .408
6 767 974 0 209 211 207 47 763 570 267 255 558 0 180 305 303 107 532 468 1000 447 979 .66 50 0 -.704 -.778 .343 .406 100 100 83 58 2.858 1.629 .35 .332 1.586 .614 .583 .41 1030 1022 104 12 2390 8020 27 32 92 97 -.704
7 1410 1597 0 645 198 187 45 1463 1733 1441 1283 1575 0 700 306 292 111 512 2528 3040 2251 2763 .95 70 0 .789 .675 .936 .971 100 100 100 100 1.015 .579 .985 .91 1.376 1.728 1.596 1.027 2904 2693 227 32 2540 8020 26 33 106 113 .789
8 889 1093 0 619 219 204 76 915 494 197 184 481 0 196 308 297 102 521 346 867 323 844 .66 60 0 -1.405 -1.462 .218 .209 87 87 71 43 4.645 2.647 .215 .207 1.92 .378 .363 .221 1112 1073 176 32 2680 8030 28 34 121 127 -1.405
9 1019 1208 0 478 196 189 48 938 787 506 479 760 0 351 294 281 104 493 888 1381 840 1333 .61 70 0 -.079 -.278 .528 .481 100 96 93 78 1.854 1.057 .539 .47 2.225 .946 .825 .597 1444 1498 227 32 2830 8020 26 33 135 142 -.079
10 739 940 0 194 219 201 80 711 540 255 235 520 0 165 294 285 103 500 447 947 412 912 .67 70 0 -.668 -.842 .331 .337 100 100 78 56 2.788 1.589 .359 .318 1.858 .629 .558 .4 966 974 232 32 2970 8020 26 33 149 156 -.668
11 3356 3549 0 2458 205 193 66 3783 1031 737 723 1017 0 583 296 294 93 516 1293 1809 1268 1784 .91 60 0 -1.549 -1.404 .139 .189 100 100 78 75 5.133 2.926 .195 .215 2.587 .342 .378 .199 4520 4079 170 32 3120 8020 27 33 165 171 -1.549
12 2700 2884 0 3101 189 184 43 3554 1995 1709 1349 1635 0 1481 290 286 102 502 2998 3500 2367 2868 .97 80 0 -.245 -.19 .511 .499 98 98 92 84 2.08 1.185 .481 .5 1.57 .844 .877 .472 5263 4049 289 52 3280 8030 27 35 180 188 -.245
13 986 1174 0 331 191 188 37 1004 749 492 484 741 0 290 271 257 95 451 863 1314 849 1300 .81 70 0 -.218 -.216 .401 .508 100 100 93 90 2.041 1.163 .49 .491 2.304 .86 .861 .514 1496 1470 221 32 3420 8020 26 33 194 201 -.218
14 888 1081 0 191 200 193 47 820 1050 762 760 1048 0 315 302 288 104 505 1337 1842 1333 1839 .84 50 0 .705 .586 .867 .85 100 100 100 91 1.076 .613 .929 .856 1.603 1.63 1.502 1.025 1582 1648 104 12 3560 8020 27 32 209 214 .705
15 1972 2163 0 1243 197 191 46 1870 4629 4334 5145 5440 0 2590 308 295 109 518 7604 8121 9026 9544 .98 80 0 2.024 2.194 2.621 2.463 94 92 98 94 .431 .246 2.318 2.609 1.808 4.066 4.577 2.242 6204 7117 298 52 3700 8030 27 35 222 230 2.024
16 10358 10547 0 6703 200 189 63 10616 12236 11941 12107 12402 0 8095 302 295 107 518 20949 21467 21240 21758 .99 80 0 .981 1.036 1.221 1.126 98 98 100 100 .889 .507 1.125 1.169 1.821 1.973 2.051 1.16 22557 22465 275 52 3860 8020 26 34 238 246 .981
17 1882 2068 0 789 193 186 48 1704 4794 4492 4311 4613 0 2260 311 302 106 530 7881 8411 7563 8093 .96 80 0 2.209 2.007 2.651 2.62 96 96 100 100 .379 .216 2.636 2.291 1.412 4.625 4.019 2.775 6196 6193 266 52 4000 8020 26 34 252 260 2.209
18 789 974 0 300 191 185 37 781 483 179 167 471 0 178 301 304 90 533 314 847 293 826 .52 60 0 -1.314 -1.429 .259 .279 100 100 75 43 4.363 2.487 .229 .212 1.854 .402 .371 .241 960 956 170 32 4150 8020 27 33 268 274 -1.314
19 2071 2261 0 1443 196 190 52 2158 844 555 464 753 0 459 295 289 101 507 974 1481 814 1321 .91 70 0 -1.148 -1.347 .238 .262 100 100 81 68 3.888 2.216 .257 .224 1.783 .451 .393 .266 2713 2535 227 32 4290 8020 26 33 281 288 -1.148
20 2441 2626 0 1059 196 185 56 2418 1670 1372 1433 1731 0 809 308 298 100 523 2407 2930 2514 3037 .94 70 0 -.007 .043 .508 .556 100 100 100 100 1.762 1.005 .567 .587 1.464 .995 1.03 .592 3790 3874 220 32 4440 8020 26 33 296 303 -.007

Total number of rows: 43008

Table truncated, full table size 9636 Kbytes.




Supplementary data files not provided
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