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Sample GSM6266 Query DataSets for GSM6266
Status Public on Apr 15, 2004
Title AML 28
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 28
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=3.574.63
Lot batch = shcz075
 
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
1 190 359 0 145 169 169 36 222 4706 4595 4346 4457 0 2169 115 111 34 125 5163 5288 4883 5008 .9 100 0 4.54 4.684 20.83 22.123 92 86 100 100 .048 .043 20.698 22.874 1.534 23.256 25.701 20.368 4817 4536 444 80 1860 7780 49 59 29 39 4.54
2 3848 4016 0 1426 170 168 36 3738 416 306 311 421 0 133 113 110 32 124 344 467 349 473 .94 80 0 -3.443 -3.461 .079 .087 100 100 100 98 12.216 10.872 .082 .081 1.381 .092 .091 .079 4044 4159 228 52 2010 7790 51 59 45 53 -3.443
3 2410 2583 0 1042 180 173 57 2350 1316 1205 1278 1389 0 506 117 111 47 125 1354 1479 1436 1561 .97 80 0 -.796 -.747 .516 .506 100 100 100 100 1.95 1.736 .513 .53 1.29 .576 .596 .496 3555 3688 230 52 2150 7790 51 59 59 67 -.796
4 632 803 0 378 178 171 54 678 310 193 195 312 0 104 121 117 44 131 217 348 219 351 .87 90 0 -1.645 -1.528 .31 .292 96 96 92 82 3.513 3.127 .285 .309 1.85 .32 .347 .27 871 827 324 52 2300 7780 49 58 73 82 -1.645
5 282 450 0 114 171 168 38 292 394 278 273 389 0 97 119 116 36 130 312 443 307 437 .83 90 0 .097 .121 .962 1.027 100 100 100 100 1.05 .935 .952 .968 1.507 1.07 1.088 .881 570 555 300 52 2440 7780 49 58 87 96 .097
6 271 441 0 136 174 170 38 304 292 184 184 292 0 77 113 108 33 121 207 328 207 328 .77 70 0 -.556 -.39 .601 .518 100 100 100 93 1.652 1.47 .605 .679 1.699 .68 .763 .532 488 455 224 32 2590 7780 50 57 103 110 -.556
7 439 606 0 214 172 167 37 455 2192 2081 2085 2196 0 780 116 111 35 125 2338 2463 2343 2467 .93 90 0 2.361 2.416 4.731 4.716 100 100 100 100 .219 .195 4.574 4.749 1.373 5.139 5.336 4.622 2536 2524 337 52 2740 7780 49 58 117 126 2.361
8 387 554 0 141 176 167 55 401 821 711 748 858 0 250 113 110 35 124 799 922 840 964 .89 90 0 .994 1.119 1.759 1.695 100 100 100 100 .564 .502 1.773 1.933 1.484 1.992 2.172 1.863 1112 1135 320 52 2880 7790 50 59 131 140 .994
9 126 295 0 74 173 169 41 133 166 57 46 155 0 37 111 109 31 122 64 187 52 174 .49 80 0 -1.054 -1.286 .44 .481 90 73 82 36 2.333 2.077 .429 .365 2.231 .482 .41 .344 190 172 254 52 3030 7790 51 59 147 155 -1.054
10 329 502 0 115 175 173 39 355 131 25 29 135 0 32 110 106 32 119 28 147 33 152 .21 90 0 -3.66 -3.336 .1 .115 100 100 42 7 14.2 12.638 .07 .088 2.081 .079 .099 .042 380 358 294 52 3170 7790 50 59 160 169 -3.66
11 1393 1567 0 521 178 174 42 1402 249 139 131 241 0 78 113 110 33 124 156 280 147 271 .79 70 0 -3.166 -3.242 .09 .093 100 100 93 81 10.086 8.977 .099 .094 1.826 .111 .106 .095 1541 1524 220 32 3310 7790 51 58 175 182 -3.166
12 2151 2323 0 1086 174 172 36 2132 2598 2486 2349 2461 0 1173 115 112 32 126 2793 2919 2639 2765 .97 80 0 .39 .295 1.19 1.146 100 100 100 100 .858 .763 1.166 1.092 1.242 1.31 1.227 1.144 4618 4500 293 52 3470 7790 51 59 191 199 .39
13 665 840 0 283 175 175 33 689 1212 1104 1157 1265 0 413 113 108 32 121 1240 1362 1300 1421 .95 80 0 .848 .967 1.647 1.651 100 98 100 100 .624 .555 1.602 1.74 1.394 1.8 1.955 1.597 1793 1822 234 52 3620 7790 51 59 206 214 .848
14 55 226 0 46 171 171 36 58 186 76 82 192 0 55 112 110 30 124 85 209 92 216 .37 70 0 .558 .744 1.522 1.316 65 34 71 62 .763 .679 1.31 1.491 3.043 1.472 1.675 1.082 134 137 191 32 3750 7790 51 58 219 226 .558
15 139 313 0 83 174 174 35 138 7906 7795 7749 7860 0 3701 111 111 29 125 8758 8883 8707 8831 .84 100 0 5.988 5.969 51.918 57.613 90 83 100 100 .018 .016 56.486 55.748 1.473 63.467 62.638 58.892 7933 7888 364 80 3910 7790 50 60 234 244 5.988
16 5908 6083 0 2773 175 175 38 4968 6153 6039 7026 7140 0 3021 117 114 35 128 6785 6913 7894 8022 .99 100 0 .45 .418 1.321 1.187 100 100 100 100 .823 .732 1.216 1.189 1.386 1.366 1.336 1.178 11007 12934 339 80 4050 7790 50 60 248 258 .45
17 1100 1277 0 610 177 177 39 1027 5535 5418 5849 5966 0 2763 117 117 32 131 6088 6219 6572 6703 .95 100 0 2.567 2.579 5.992 5.406 97 93 100 100 .19 .169 5.276 5.317 1.661 5.928 5.974 5.278 6445 6949 378 80 4200 7790 50 60 263 273 2.567
18 182 352 0 78 173 170 38 188 142 25 24 141 0 39 115 117 30 131 28 160 27 158 .24 70 0 -2.743 -2.755 .189 .195 96 96 40 12 7.52 6.693 .133 .132 3.452 .149 .148 .103 213 206 212 32 4350 7790 51 58 279 286 -2.743
19 895 1061 0 332 172 166 39 894 497 383 387 501 0 134 120 114 57 128 430 558 435 563 .94 70 0 -1.055 -1.041 .44 .437 100 100 100 100 2.334 2.077 .428 .432 1.353 .481 .486 .411 1277 1282 218 32 4500 7790 51 58 294 301 -1.055
20 610 775 0 356 171 165 40 586 484 370 339 453 0 206 116 114 32 128 416 544 381 509 .92 80 0 -.495 -.679 .712 .695 94 94 98 90 1.584 1.41 .631 .556 1.826 .709 .624 .594 956 949 251 52 4650 7790 51 59 309 317 -.495

Total number of rows: 43008

Table truncated, full table size 9154 Kbytes.




Supplementary data files not provided
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