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Sample GSM6327 Query DataSets for GSM6327
Status Public on Apr 15, 2004
Title AML 84
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 84
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=760640LaserPower=4.424.59
Lot batch = shdj094
 
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
1 388 500 0 184 116 112 28 388 630 490 447 587 0 306 145 140 65 171 598 768 545 716 .88 60 0 .623 .491 1.089 1.193 96 96 90 90 .792 .649 1.263 1.152 2.047 1.54 1.405 1.475 878 835 164 32 1590 8290 26 32 20 26 .623
2 2318 2427 0 1317 112 109 25 2348 3115 2971 3049 3193 0 1476 149 144 63 176 3623 3799 3718 3894 .96 80 0 .626 .682 1.429 1.258 98 96 100 100 .79 .648 1.265 1.315 1.89 1.543 1.604 1.233 5319 5367 288 52 1730 8290 25 33 33 41 .626
3 690 806 0 453 126 116 65 888 1124 983 977 1118 0 535 155 141 74 172 1199 1371 1191 1363 .94 50 0 .433 .788 1.047 .983 100 100 100 100 .903 .741 1.107 1.416 1.493 1.35 1.727 1.099 1871 1667 104 12 1890 8280 25 30 50 55 .433
4 524 633 0 310 112 109 25 491 516 384 369 501 0 263 141 132 57 161 468 629 450 611 .9 60 0 -.068 -.22 .785 .732 100 90 93 84 1.279 1.048 .782 .704 1.729 .954 .859 .791 875 893 159 32 2030 8290 26 32 64 70 -.068
5 820 929 0 470 110 109 23 725 1624 1482 1443 1585 0 765 147 142 58 173 1807 1980 1760 1933 .94 80 0 1.318 1.102 2.461 2.148 94 90 100 100 .489 .401 2.044 1.76 2.033 2.493 2.146 1.972 2207 2263 262 52 2170 8280 24 32 77 85 1.318
6 485 586 0 211 107 101 23 488 685 556 619 748 0 221 138 129 57 157 678 835 755 912 .9 60 0 .475 .638 1.125 1.141 100 100 100 93 .878 .72 1.139 1.276 1.452 1.389 1.556 1.106 1044 1104 171 32 2310 8290 26 32 92 98 .475
7 863 973 0 562 112 110 24 841 1281 1130 1046 1197 0 673 154 151 63 184 1378 1562 1276 1460 .92 80 0 .712 .564 1.527 1.338 98 96 100 98 .744 .61 1.344 1.212 2.077 1.639 1.478 1.324 1971 1909 276 52 2460 8290 25 33 106 114 .712
8 385 495 0 233 112 110 30 445 435 296 258 397 0 224 149 139 66 170 361 530 315 484 .77 60 0 -.302 -.291 .598 .619 96 96 87 71 1.503 1.233 .665 .67 2.031 .811 .817 .735 741 643 170 32 2600 8290 26 32 121 127 -.302
9 374 483 0 168 113 109 26 363 467 335 345 477 0 164 139 132 60 161 409 570 421 582 .81 80 0 .17 .17 .889 .926 96 94 98 92 1.084 .889 .923 .922 1.686 1.125 1.125 .889 698 719 287 52 2750 8280 24 32 135 143 .17
10 339 445 0 169 109 106 25 338 474 334 306 446 0 186 143 140 53 171 407 578 373 544 .86 70 0 .269 .139 .997 .847 100 96 100 90 1.012 .83 .988 .903 1.837 1.205 1.101 1.031 672 645 212 32 2890 8280 24 31 149 156 .269
11 2950 3059 0 1247 111 109 26 2774 977 845 794 926 0 416 142 132 57 161 1030 1191 968 1129 .91 80 0 -1.429 -1.607 .329 .312 100 98 98 96 3.283 2.692 .305 .269 2.042 .371 .328 .282 3619 3744 285 52 3040 8280 24 32 164 172 -1.429
12 5730 5839 0 2778 113 109 27 4919 6352 6216 6618 6754 0 2893 144 136 59 166 7580 7746 8071 8237 .98 90 0 .624 .494 1.511 1.271 100 100 100 100 .791 .649 1.264 1.155 1.84 1.541 1.409 1.187 11135 12348 312 52 3190 8280 23 32 178 187 .624
13 515 627 0 302 115 112 30 576 3982 3855 3646 3773 0 2072 141 127 59 155 4701 4856 4446 4601 .91 90 0 3.029 3.11 6.34 6.75 98 98 100 100 .149 .123 6.693 7.08 1.535 8.162 8.634 6.844 4431 4161 300 52 3330 8280 23 32 192 201 3.029
14 354 465 0 139 114 111 27 377 1046 912 853 987 0 427 144 134 59 163 1112 1276 1040 1204 .88 110 0 1.561 1.555 2.231 2.406 100 100 98 98 .413 .339 2.419 2.41 1.865 2.95 2.939 2.686 1289 1207 440 80 3480 8280 22 33 206 217 1.561
15 531 643 0 303 115 112 25 531 22620 22476 22976 23120 0 9560 152 144 63 176 27410 27585 28020 28195 .95 100 0 5.69 5.722 42.928 42.466 92 91 100 100 .024 .019 42.328 43.269 1.33 51.619 52.767 41.483 23007 23507 378 80 3630 8280 23 33 222 232 5.69
16 2985 3094 0 1590 115 109 37 2876 8851 8708 8262 8405 0 3813 152 143 69 174 10620 10794 10076 10250 .96 110 0 1.885 1.755 3.51 3.058 98 98 100 100 .33 .271 3.028 2.768 1.747 3.692 3.375 2.886 11584 11247 403 80 3790 8290 23 34 237 248 1.885
17 1230 1337 0 308 108 107 24 1153 14959 14824 15460 15595 0 3013 144 135 65 165 18078 18243 18854 19018 .97 110 0 3.971 3.938 13.18 12.639 100 100 100 100 .078 .064 12.857 12.569 1.241 15.679 15.328 12.843 15977 16690 367 80 3920 8280 22 33 250 261 3.971
18 6 110 0 122 107 104 24 43 188 54 44 178 0 109 144 134 61 163 66 229 54 217 .53 100 -50 3.161 1.841 1.264 35 21 31 13 .796 .653 1.256 7.333 4.91 1.531 8.943 1.262 97 50 339 80 4070 8280 23 33 266 276 .615
19 1745 1852 0 570 110 107 26 1639 933 796 810 947 0 338 140 137 56 167 971 1138 988 1155 .92 90 0 -.756 -.821 .462 .497 100 100 100 100 2.059 1.688 .486 .464 1.531 .592 .566 .462 2435 2555 271 52 4220 8270 22 31 281 290 -.756
20 978 1085 0 339 111 107 29 926 647 507 502 642 0 225 143 140 60 171 618 789 612 783 .9 110 0 -.583 -.676 .543 .523 98 98 97 96 1.826 1.498 .548 .513 1.547 .668 .626 .54 1433 1480 387 80 4360 8290 23 34 294 305 -.583

Total number of rows: 43008

Table truncated, full table size 9168 Kbytes.




Supplementary data files not provided
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