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Sample GSM6300 Query DataSets for GSM6300
Status Public on Apr 15, 2004
Title AML 97
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 97
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=660650LaserPower=3.874.1
Lot batch = shdj067
 
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 GPL319
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
1 343 460 0 277 121 117 30 382 969 881 835 923 0 404 91 88 28 121 1207 1327 1144 1264 .92 80 0 1.66 1.738 2.682 2.52 98 92 100 100 .434 .317 2.306 2.434 1.614 3.159 3.335 2.111 1263 1178 268 52 2180 8960 28 36 22 30 1.66
2 4081 4202 0 1880 125 121 35 3809 1833 1741 1707 1799 0 800 93 92 29 126 2385 2511 2338 2464 .98 80 0 -.675 -.803 .485 .458 100 100 100 100 2.188 1.597 .457 .418 1.422 .626 .573 .443 5550 5788 254 52 2320 8970 29 37 36 44 -.675
3 954 1073 0 618 122 119 30 1031 503 412 341 432 0 267 93 91 28 125 564 689 467 592 .97 60 0 -.869 -1.03 .398 .401 100 100 100 100 2.502 1.827 .4 .357 1.465 .547 .49 .407 1443 1295 170 32 2470 8960 29 35 52 58 -.869
4 646 767 0 284 126 121 33 666 319 233 229 315 0 106 90 86 28 118 319 437 314 432 .9 60 0 -1.061 -1.042 .349 .357 100 100 100 100 2.858 2.087 .35 .354 1.289 .479 .486 .313 899 875 164 32 2610 8960 29 35 66 72 -1.061
5 1083 1204 0 609 124 121 33 1162 882 794 758 846 0 408 91 88 29 121 1088 1208 1038 1159 .96 80 0 -.095 -.061 .657 .654 100 100 100 98 1.463 1.068 .683 .7 1.488 .936 .959 .664 1956 1841 286 52 2760 8960 28 36 80 88 -.095
6 490 611 0 320 123 121 34 510 900 815 856 941 0 445 88 85 29 116 1116 1233 1173 1289 .95 80 0 1.13 1.259 1.656 1.612 100 98 100 100 .626 .457 1.598 1.747 1.533 2.189 2.393 1.539 1325 1346 267 52 2910 8960 28 36 95 103 1.13
7 1497 1616 0 654 128 119 79 1334 1030 935 889 984 0 402 99 95 54 130 1281 1411 1218 1348 .97 70 0 -.059 -.298 .724 .693 100 100 100 100 1.427 1.042 .701 .594 1.287 .96 .813 .643 2269 2386 210 32 3050 8970 29 36 109 116 -.059
8 502 623 0 266 125 121 44 512 229 132 134 231 0 69 101 97 38 133 181 314 184 316 .83 80 0 -1.502 -1.451 .271 .257 98 98 86 78 3.879 2.832 .258 .267 1.835 .353 .366 .237 644 636 268 52 3200 8950 27 35 124 132 -1.502
9 401 520 0 174 121 119 32 413 1305 1212 1233 1326 0 408 96 93 30 127 1660 1788 1689 1816 .94 90 0 2.007 2.075 3.051 2.901 100 100 100 100 .341 .249 2.935 3.075 1.355 4.02 4.212 3.042 1625 1634 324 52 3340 8950 26 35 137 146 2.007
10 252 371 0 115 120 119 29 243 192 105 97 184 0 57 91 87 27 119 144 263 133 252 .61 70 0 -.757 -.923 .422 .407 100 90 96 75 2.314 1.689 .432 .385 2.434 .592 .527 .348 348 349 206 32 3490 8950 27 34 153 160 -.757
11 3468 3587 0 1393 123 119 35 3390 421 327 340 434 0 134 95 94 29 129 448 577 466 595 .93 80 0 -2.92 -2.896 .101 .102 100 100 98 98 10.367 7.568 .096 .098 1.473 .132 .134 .09 3717 3808 276 52 3630 8950 27 35 167 175 -2.92
12 7045 7162 0 3497 125 117 66 6452 4922 4829 5396 5489 0 2402 114 93 272 127 6615 6742 7392 7519 .98 90 0 .036 .069 .802 .758 100 98 100 100 1.336 .975 .748 .766 1.62 1.025 1.049 .731 11281 12441 325 52 3780 8950 26 35 181 190 .036
13 1055 1174 0 426 124 119 40 954 729 639 712 802 0 277 96 90 40 123 875 999 975 1099 .96 90 0 -.124 -.113 .687 .673 98 98 100 98 1.493 1.09 .67 .675 1.55 .918 .924 .654 1593 1767 285 52 3920 8950 26 35 195 204 -.124
14 268 388 0 123 128 120 53 285 485 396 369 458 0 228 91 89 31 122 542 664 505 627 .83 120 0 .929 .915 1.276 1.272 97 91 98 97 .72 .525 1.389 1.377 1.935 1.903 1.886 1.648 681 637 484 120 4080 8950 25 37 210 222 .929
15 897 1015 0 347 124 118 35 857 1681 1593 1741 1829 0 665 90 88 31 121 2182 2303 2385 2505 .97 100 0 1.348 1.411 1.832 1.857 100 100 100 100 .538 .393 1.859 1.941 1.229 2.546 2.659 1.892 2450 2638 290 80 4220 8950 26 36 225 235 1.348
16 4816 4931 0 2596 119 115 37 4780 7962 7873 7818 7907 0 3974 94 89 37 122 10785 10907 10710 10832 .98 120 0 1.174 1.153 1.726 1.622 98 98 100 100 .607 .443 1.647 1.623 1.398 2.256 2.224 1.626 12653 12634 443 120 4370 8950 25 37 239 251 1.174
17 1737 1854 0 396 121 117 36 1657 9096 9010 9496 9582 0 2033 102 86 93 118 12342 12460 13008 13126 .97 110 0 2.897 2.905 5.456 5.434 100 100 100 100 .184 .134 5.438 5.467 1.181 7.449 7.489 5.394 10667 11233 360 80 4510 8940 24 35 253 264 2.897
18 8 125 0 122 124 117 37 42 123 39 27 111 0 67 97 84 96 115 53 168 37 152 .6 100 -50 2.209 .94 .703 28 8 10 5 1.077 .786 .929 3.375 3.551 1.272 4.623 .475 81 35 319 80 4660 8940 25 35 269 279 .347
19 2224 2343 0 1068 122 119 31 2155 983 898 943 1028 0 420 101 85 108 116 1230 1347 1292 1408 .97 100 0 -.809 -.784 .427 .42 100 98 97 92 2.4 1.752 .417 .424 1.541 .571 .581 .402 3053 3167 276 80 4810 8950 26 36 284 294 -.809
20 997 1115 0 532 121 118 32 986 889 799 862 952 0 375 100 90 88 123 1095 1218 1181 1304 .96 120 0 .151 .244 .894 .814 97 96 98 94 1.234 .901 .81 .865 1.858 1.11 1.184 .773 1785 1859 423 120 4950 8940 24 36 297 309 .151

Total number of rows: 43008

Table truncated, full table size 9118 Kbytes.




Supplementary data files not provided
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