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Sample GSM6302 Query DataSets for GSM6302
Status Public on Apr 15, 2004
Title AML 50
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 50
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=720650LaserPower=3.94.53
Lot batch = shdj069
 
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
1 396 525 0 322 133 129 33 456 3820 3690 3805 3935 0 2386 136 130 52 141 4011 4152 4136 4277 .92 80 0 3.137 3.385 7.648 7.737 86 86 100 100 .124 .114 8.092 9.609 1.874 8.796 10.444 8.42 4146 4201 278 52 1590 8720 32 40 19 27 3.137
2 3914 4050 0 2293 138 136 33 3930 919 794 857 982 0 446 136 125 52 136 863 999 932 1067 .92 80 0 -2.187 -2.071 .215 .211 100 100 98 90 4.95 4.554 .202 .219 2.099 .22 .238 .183 4724 4771 285 52 1740 8710 31 39 34 42 -2.187
3 927 1062 0 1268 136 135 31 1501 1450 1319 948 1079 0 990 138 131 49 142 1434 1576 1030 1173 .93 60 0 -.066 .153 .809 .844 100 93 93 93 1.138 1.047 .879 1.023 2.991 .955 1.112 .815 2820 1875 170 32 1890 8720 33 39 50 56 -.066
4 883 1009 0 473 136 126 45 870 646 517 530 659 0 272 140 129 50 140 562 702 576 716 .87 60 0 -.631 -.616 .629 .605 100 96 96 90 1.683 1.548 .594 .6 1.717 .646 .652 .538 1387 1413 151 32 2040 8720 33 39 65 71 -.631
5 989 1123 0 665 138 134 34 1102 2729 2596 2486 2619 0 1314 139 133 51 145 2822 2966 2702 2847 .94 80 0 1.356 1.45 2.671 2.37 98 96 100 100 .424 .391 2.356 2.514 1.902 2.561 2.732 2.333 3698 3475 277 52 2180 8710 31 39 78 86 1.356
6 653 790 0 476 140 137 37 643 1503 1367 1358 1494 0 982 144 136 57 148 1486 1634 1476 1624 .91 80 0 1.208 1.177 2.226 2.073 86 80 94 92 .47 .433 2.126 2.08 2.491 2.311 2.26 2.224 2010 2011 264 52 2330 8710 31 39 93 101 1.208
7 1129 1267 0 1400 142 138 36 1483 2620 2479 2200 2341 0 2036 144 141 52 153 2695 2848 2391 2545 .93 80 0 .862 1.083 2.017 1.586 88 86 100 96 .598 .55 1.672 1.949 2.354 1.817 2.118 1.597 3962 3329 264 52 2470 8720 32 40 107 115 .862
8 781 915 0 311 135 134 32 850 423 285 254 392 0 128 142 138 53 150 310 460 276 426 .81 70 0 -1.456 -1.5 .312 .341 100 100 93 90 2.982 2.744 .335 .325 1.815 .364 .354 .326 1135 1035 214 32 2620 8720 32 39 122 129 -1.456
9 439 573 0 261 135 134 35 421 433 301 292 424 0 181 189 132 658 143 327 471 317 461 .83 90 0 -.364 -.468 .702 .683 90 88 0 0 1.399 1.287 .715 .665 1.651 .777 .723 .66 722 731 350 52 2760 8710 30 39 135 144 -.364
10 302 438 0 143 141 136 50 315 287 146 168 309 0 69 322 141 1199 153 159 312 183 336 .06 50 0 -.989 -.726 .452 .382 100 91 0 0 2.158 1.985 .463 .556 2.256 .504 .605 51.073 461 470 104 12 2910 8710 32 37 152 157 -.989
11 3255 3385 0 2347 140 130 56 3443 924 789 669 804 0 573 142 135 52 147 858 1004 727 874 .87 100 0 -2.005 -2.162 .226 .233 98 96 95 90 4.364 4.015 .229 .206 2.018 .249 .223 .206 4232 3924 409 80 3060 8720 31 41 165 175 -2.005
12 6970 7099 0 4263 140 129 62 7397 12474 12335 11404 11543 0 6525 154 139 102 151 13408 13559 12396 12547 .93 90 0 .858 .831 1.801 1.603 100 98 100 100 .6 .552 1.668 1.636 1.955 1.813 1.778 1.662 19732 18374 289 52 3200 8710 30 39 179 188 .858
13 808 940 0 640 141 132 57 908 1568 1431 1223 1360 0 915 151 137 95 149 1555 1704 1329 1478 .9 100 0 .777 .718 1.638 1.512 88 85 98 96 .635 .584 1.576 1.514 1.954 1.713 1.645 1.577 2339 2031 377 80 3350 8720 31 41 194 204 .777
14 227 358 0 134 136 131 36 248 781 646 614 749 0 294 140 135 56 147 702 849 667 814 .64 110 0 1.501 1.556 2.701 2.456 98 95 100 100 .384 .353 2.605 2.705 2.213 2.831 2.94 3.29 894 841 417 80 3500 8720 30 41 208 219 1.501
15 940 1067 0 540 133 127 34 863 4441 4302 4743 4882 0 1941 142 139 56 151 4676 4827 5155 5307 .93 110 0 2.438 2.455 5.444 5.02 88 85 100 100 .201 .185 4.985 5.046 1.735 5.418 5.485 4.857 5165 5683 376 80 3650 8720 30 41 223 234 2.438
16 5844 5972 0 2910 131 128 33 5428 14097 13963 14682 14816 0 6597 143 134 54 146 15177 15323 15959 16104 .92 110 0 1.483 1.449 2.866 2.614 98 98 100 100 .389 .358 2.572 2.512 1.692 2.796 2.731 2.634 19391 20526 350 80 3780 8720 30 41 236 247 1.483
17 1644 1774 0 898 133 130 34 1487 8730 8594 9920 10056 0 4342 141 136 54 148 9341 9489 10783 10930 .89 120 0 2.651 2.713 6.128 5.796 92 90 100 100 .173 .159 5.779 6.034 2.034 6.282 6.559 6.056 10081 11564 410 120 3930 8720 30 42 251 263 2.651
18 1 126 0 144 131 125 33 41 206 69 35 172 0 125 141 137 52 149 75 224 38 187 .58 100 -50 5.25 1.482 1.556 30 17 40 20 .594 .547 1.683 35 3.574 1.829 38.043 1.021 110 36 320 80 4080 8710 30 40 267 277 .871
19 4447 4574 0 1828 141 127 125 4021 4040 3895 4145 4290 0 1549 156 145 84 158 4234 4391 4505 4663 .93 90 0 .074 .019 1.061 .983 98 98 100 100 1.032 .95 .969 .932 1.712 1.053 1.013 .911 7916 8592 278 52 4220 8710 30 39 281 290 .074
20 2216 2348 0 928 142 132 109 2188 3020 2880 2976 3116 0 960 152 140 78 152 3130 3283 3235 3387 .92 110 0 .517 .546 1.451 1.285 98 95 100 100 .76 .699 1.316 1.343 1.655 1.431 1.46 1.275 5068 5192 375 80 4370 8720 30 41 295 306 .517

Total number of rows: 43008

Table truncated, full table size 9485 Kbytes.




Supplementary data files not provided
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