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Sample GSM6294 Query DataSets for GSM6294
Status Public on Apr 15, 2004
Title AML 110
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 110
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=710650LaserPower=4.023.13
Lot batch = shcz092
 
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
1 222 365 0 230 151 143 36 260 877 730 674 821 0 409 153 147 59 175 869 1044 802 977 .85 90 0 1.741 1.854 3.18 2.811 80 75 96 94 .356 .299 2.808 3.036 2.53 3.342 3.614 2.718 990 896 348 52 1950 7690 28 37 22 31 1.741
2 2357 2511 0 1368 174 154 84 2222 548 396 333 485 0 357 161 152 64 181 471 652 396 577 .91 90 0 -2.237 -2.572 .149 .167 94 94 73 69 5.611 4.713 .178 .141 1.769 .212 .168 .198 2618 2690 290 52 2090 7690 28 37 36 45 -2.237
3 1575 1734 0 1100 171 159 78 1511 1404 1253 1282 1433 0 856 156 151 58 180 1492 1671 1526 1706 .97 80 0 -.019 -.045 .893 .848 84 82 94 86 1.206 1.013 .829 .814 1.672 .987 .969 .801 2764 2857 270 52 2230 7690 29 37 51 59 -.019
4 688 844 0 273 157 156 40 631 481 335 340 486 0 191 154 146 52 174 399 573 405 579 .88 60 0 -.662 -.765 .491 .52 93 93 93 90 1.884 1.582 .531 .494 1.602 .632 .588 .551 966 1028 176 32 2380 7690 30 36 67 73 -.662
5 1092 1309 0 257 594 217 2198 1038 2071 1866 1889 2094 0 523 265 205 264 244 2221 2465 2249 2493 .45 50 0 1.098 1.042 1.779 1.79 0 0 100 100 .556 .467 1.798 1.73 1.229 2.14 2.059 .638 2904 2981 104 12 2540 7680 29 34 83 88 1.098
6 930 1085 0 308 176 155 91 809 638 488 498 648 0 286 168 150 78 179 581 760 593 771 .91 50 0 -.478 -.65 .595 .603 100 100 91 91 1.658 1.393 .603 .535 1.404 .718 .637 .654 1297 1428 104 12 2660 7680 29 34 95 100 -.478
7 1006 1151 0 581 155 145 56 932 2796 2658 2956 3094 0 1449 149 138 56 164 3164 3329 3519 3683 .96 90 0 1.763 1.807 3.048 2.698 92 90 100 100 .351 .295 2.852 2.938 1.588 3.395 3.498 2.819 3590 3962 340 52 2820 7690 28 37 109 118 1.763
8 477 618 0 264 150 141 50 415 350 215 222 357 0 149 146 135 56 161 256 417 264 425 .76 90 0 -.697 -.852 .451 .517 88 86 80 71 1.93 1.621 .518 .465 2.178 .617 .554 .479 630 699 304 52 2960 7690 28 37 123 132 -.697
9 404 545 0 231 147 141 42 408 379 248 256 387 0 143 138 131 48 156 295 451 305 461 .88 60 0 -.467 -.407 .572 .636 93 90 90 87 1.645 1.382 .608 .634 1.81 .724 .754 .591 656 660 165 32 3100 7690 30 36 139 145 -.467
10 440 586 0 212 154 146 45 411 244 114 94 224 0 98 136 130 47 155 136 290 112 267 .65 90 0 -1.599 -1.975 .257 .284 90 88 82 50 3.605 3.028 .277 .214 2.121 .33 .254 .261 525 534 313 52 3250 7700 29 38 152 161 -1.599
11 1604 1745 0 1474 150 141 43 1684 690 555 450 585 0 477 137 135 49 161 661 821 536 696 .95 80 0 -1.35 -1.582 .355 .341 88 84 88 80 3.034 2.549 .33 .281 2.186 .392 .334 .316 2239 2054 276 52 3400 7690 29 37 168 176 -1.35
12 2658 2802 0 1798 146 144 36 2658 3880 3753 4070 4197 0 2330 133 127 49 151 4468 4619 4845 4996 .98 90 0 .749 .866 1.624 1.406 94 94 100 100 .708 .595 1.412 1.531 1.55 1.681 1.823 1.375 6411 6728 301 52 3550 7690 28 37 182 191 .749
13 699 840 0 490 146 141 33 677 1502 1369 1374 1507 0 852 138 133 48 158 1630 1788 1636 1794 .95 80 0 1.267 1.227 2.2 2.077 88 82 100 94 .495 .415 2.022 1.966 1.649 2.407 2.34 1.939 2046 2073 259 52 3690 7690 29 37 197 205 1.267
14 338 473 0 120 134 135 33 331 451 319 314 446 0 143 138 132 54 157 380 537 374 531 .79 50 0 .198 .145 .941 .942 100 100 100 91 1.038 .872 .964 .929 1.796 1.147 1.106 1.118 650 652 104 12 3830 7680 29 34 212 217 .198
15 330 463 0 249 135 133 33 323 10888 10760 10055 10183 0 7037 139 128 80 152 12810 12962 11970 12123 .97 100 0 5.31 5.181 32.811 30.97 83 75 100 100 .03 .025 33.313 30.47 1.399 39.658 36.273 31.948 11083 10385 410 80 3980 7690 28 38 225 235 5.31
16 4218 4359 0 2136 1595 141 6049 3899 11082 10941 11973 12114 0 5544 598 141 2071 168 13025 13193 14254 14421 .59 80 0 1.74 1.757 3.024 2.74 19 0 92 84 .356 .299 2.806 2.839 1.599 3.341 3.379 2.368 14840 16191 277 52 4130 7680 28 36 241 249 1.74
17 637 784 0 436 3288 147 9226 617 8898 8750 8560 8708 0 4641 1282 148 4023 176 10417 10593 10190 10367 .43 100 0 4.077 4 14.823 13.487 0 0 81 53 .071 .059 14.182 13.438 1.72 16.883 15.998 .482 9367 9197 340 80 4300 7710 30 40 257 267 4.077
18 331 461 0 214 142 130 71 365 255 126 122 251 0 100 137 129 51 154 150 304 145 299 .73 60 0 -1.283 -1.188 .358 .39 87 84 71 56 2.897 2.433 .345 .369 2.331 .411 .439 .355 491 453 142 32 4420 7690 30 36 271 277 -1.283
19 2195 2335 0 1125 148 140 54 2152 1177 1041 1040 1176 0 482 137 136 45 162 1239 1401 1238 1400 .97 70 0 -.796 -.826 .52 .483 100 100 100 100 2.067 1.736 .484 .474 1.466 .576 .564 .456 3193 3235 219 32 4570 7680 28 35 285 292 -.796
20 1595 1733 0 828 143 138 59 1360 1254 1121 1170 1303 0 609 139 133 50 158 1335 1493 1393 1551 .96 80 0 -.027 -.196 .917 .852 88 86 94 94 1.213 1.019 .824 .734 1.794 .981 .873 .779 2481 2765 276 52 4710 7690 29 37 299 307 -.027

Total number of rows: 43008

Table truncated, full table size 9420 Kbytes.




Supplementary data files not provided
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