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Sample GSM6228 Query DataSets for GSM6228
Status Public on Apr 15, 2004
Title AML 104
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 104
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=4.394.29
Lot batch = shco019
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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 GPL317
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 �m 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 two standard deviations above the background pixel intensity, at Channel 1
PERGTBCH2I_2SD Percentage of spot pixels with intensities more than two standard deviations above the background pixel intensity, at Channel 2
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 �m 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 �m 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
1 129 314 0 110 185 185 39 155 253 131 116 238 0 88 125 122 34 144 154 298 136 280 .61 70 0 -.008 .081 .935 .875 87 75 87 81 1.183 1.006 .845 .899 2.751 .994 1.058 .755 286 245 218 32 2750 7530 93 100 55 62 -.008
2 164 339 0 394 181 175 40 254 208 85 49 172 0 141 126 123 35 145 100 245 58 202 .6 80 -100 -1.508 .34 .318 96 86 63 36 2.988 2.54 .335 .299 2.504 .394 .352 .245 339 213 259 52 2930 7520 92 100 73 81 -1.345
3 577 750 0 731 177 173 35 768 197 70 43 170 0 84 133 127 43 149 82 232 51 200 .45 90 0 -3.221 -3.512 .109 .119 94 92 50 28 10.971 9.326 .091 .075 2.896 .107 .088 .057 838 620 294 52 3070 7520 91 100 86 95 -3.221
4 719 897 0 1751 178 178 35 1431 1096 977 587 706 0 950 123 119 35 140 1149 1289 691 831 .82 90 -100 -.058 1.038 .769 82 76 90 84 1.465 1.245 .683 .816 4.532 .803 .96 .531 2408 1306 276 52 3240 7520 91 100 103 112 -.316
5 28 214 0 214 192 186 53 105 207 81 30 156 0 141 129 126 34 148 95 244 35 184 .72 100 -100 .334 1.029 .889 35 21 47 33 1.296 1.102 .771 1.071 3.617 .908 1.261 .565 186 58 416 80 3340 7500 89 99 113 123 -.14
6 165 347 0 53 185 182 35 169 180 57 52 175 0 46 127 123 33 145 67 212 61 206 .39 50 0 -1.334 -1.431 .315 .294 100 100 75 33 2.965 2.52 .337 .315 1.851 .397 .371 .264 226 217 92 12 3500 7530 94 99 131 136 -1.334
7 390 581 0 200 192 191 47 368 617 494 502 625 0 219 126 123 34 145 581 726 591 735 .79 80 0 .659 .599 1.537 1.193 94 88 100 100 .745 .633 1.342 1.287 2.477 1.579 1.514 1.281 862 892 255 52 3640 7520 92 100 144 152 .659
8 2956 3139 0 1129 191 183 51 2806 2904 2776 2743 2871 0 1133 140 128 56 151 3266 3416 3227 3378 .85 70 0 .219 .127 1.013 .896 100 100 100 100 1.011 .859 .989 .928 1.832 1.164 1.092 1.017 5582 5699 184 32 3780 7530 93 100 158 165 .219
9 404 585 0 255 187 181 49 364 2031 1903 1877 2005 0 938 134 128 45 151 2239 2389 2208 2359 .84 80 0 2.621 2.45 6.15 5.019 84 80 100 100 .191 .163 5.228 4.646 2.09 6.151 5.466 5.271 2267 2281 307 52 3940 7520 92 100 174 182 2.621
10 147 332 0 94 191 185 43 178 183 63 62 182 0 42 124 120 32 141 74 215 73 214 .26 50 0 -1.264 -1.011 .415 .57 100 75 75 41 2.825 2.402 .354 .422 3.145 .416 .496 .152 241 209 104 12 4080 7510 92 97 189 194 -1.264
11 1195 1371 0 590 183 176 65 1174 594 472 460 582 0 206 127 122 40 144 555 699 541 685 .78 110 0 -1.08 -1.143 .418 .388 100 97 100 96 2.487 2.114 .402 .385 1.93 .473 .453 .328 1646 1655 505 80 4230 7520 90 101 201 212 -1.08
12 430 602 0 226 184 172 96 496 481 359 333 455 0 212 129 122 45 144 422 566 392 535 .66 60 0 -.232 -.134 .627 .732 100 96 96 96 1.382 1.174 .724 .774 2.425 .852 .911 .664 855 763 162 32 4380 7530 94 100 219 225 -.232
13 337 507 0 111 174 170 38 346 282 164 147 265 0 71 121 118 30 139 193 332 173 312 .73 70 0 -.843 -.962 .441 .482 100 100 96 93 2.11 1.793 .474 .436 1.847 .558 .513 .431 510 484 187 32 4510 7520 92 99 231 238 -.843
14 25 194 0 66 174 169 38 40 125 0 -4 121 0 34 127 125 36 147 0 147 142 .04 100 -50 .618 .608 42 26 10 3 3.546 .056 40 21 423 80 4650 7500 89 99 244 254
15 2708 2891 0 1447 187 183 44 2719 1535 1404 1270 1401 0 722 135 131 40 154 1652 1806 1494 1648 .84 90 0 -.719 -.858 .519 .495 100 100 100 100 1.937 1.646 .516 .469 1.879 .607 .552 .46 4123 3978 287 52 4810 7520 91 100 260 269 -.719
16 891 1071 0 352 183 180 41 797 389 261 271 399 0 156 129 128 39 151 307 458 319 469 .79 80 0 -1.376 -1.483 .295 .344 98 98 86 82 3.054 2.596 .327 .304 2.235 .385 .358 .308 1058 1162 271 52 4960 7530 93 101 276 284 -1.376
17 136 300 0 75 162 164 35 156 154 30 28 152 0 40 123 124 36 146 35 181 33 179 .33 60 0 -2.144 -2.046 .302 .352 96 90 43 18 5.2 4.42 .192 .206 2.494 .226 .242 .162 186 164 171 32 5100 7520 93 99 291 297 -2.144
18 108 268 0 53 162 160 32 112 192 70 72 194 0 26 123 122 33 144 82 226 85 228 .28 50 0 -.444 -.35 .647 .675 100 83 91 58 1.6 1.36 .625 .667 1.679 .735 .784 .317 182 180 104 12 5240 7520 93 98 305 310 -.444
19 675 839 0 339 168 164 39 663 548 425 458 581 0 202 127 123 36 145 500 645 539 684 .73 120 0 -.407 -.325 .668 .653 95 92 94 90 1.56 1.326 .641 .679 3.209 .754 .798 .546 1088 1133 586 120 5400 7520 90 102 318 330 -.407
20 458 621 0 159 170 163 52 452 520 394 387 513 0 102 134 126 39 148 464 612 455 604 .74 70 0 .036 -.009 .92 .872 100 96 100 100 1.147 .975 .872 .845 1.688 1.026 .994 .726 846 845 187 32 5530 7510 91 98 333 340 .036

Total number of rows: 43008

Table truncated, full table size 8851 Kbytes.




Supplementary data files not provided
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