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Sample GSM6234 Query DataSets for GSM6234
Status Public on Apr 15, 2004
Title AML 109
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 109
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=700650LaserPower=4.144.42
Lot batch = shco026
 
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 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 �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
1 142 400 0 220 268 258 55 102 280 43 41 278 0 128 241 237 64 658 119 778 114 772 .39 60 0 .228 -.318 .429 .502 59 53 43 28 2.372 .854 .422 .289 2.604 1.171 .802 .394 145 183 160 32 1770 7900 79 85 62 68 .228
2 452 725 0 233 294 273 119 363 370 120 99 349 0 142 252 250 67 694 333 1028 275 969 .66 50 0 -.123 -.717 .268 .349 83 83 58 41 3.025 1.089 .331 .219 2.683 .918 .608 .383 483 551 92 12 1920 7890 78 83 77 82 -.123
3 1811 2068 0 899 266 257 68 1641 326 88 87 325 0 117 238 238 66 661 244 906 242 903 .54 90 0 -2.747 -2.906 .087 .082 92 92 55 38 18.648 6.713 .054 .048 2.625 .149 .133 .058 1729 1898 303 52 2030 7890 76 85 86 95 -2.747
4 2491 2730 0 2827 249 239 66 3295 1120 891 708 937 0 795 234 229 67 636 2475 3111 1967 2603 .95 80 0 -.413 -.341 .269 .263 88 86 80 73 3.698 1.331 .27 .284 2.238 .751 .79 .26 4186 3199 248 52 2190 7910 79 87 103 111 -.413
5 374 619 0 476 256 245 84 438 526 308 309 527 0 301 231 218 74 606 856 1461 858 1464 .85 60 0 .966 1.198 .71 .63 59 56 68 59 1.422 .512 .703 .826 2.031 1.953 2.295 .633 746 683 171 32 2340 7890 78 84 119 125 .966
6 9 248 0 120 245 239 65 18 267 29 40 278 0 97 272 238 218 661 81 742 111 772 .35 100 -50 3.626 .911 1 30 17 3 0 .621 .223 1.611 4.444 2.63 4.475 12.346 1.607 47 49 383 80 2490 7880 75 85 132 142 2.162
7 55 306 0 219 289 251 249 110 3476 3209 3338 3605 0 2526 362 267 513 742 8914 9656 9272 10014 .46 90 0 6.34 7.397 17.395 17.868 32 1 82 69 .034 .012 29.173 60.691 2.99 81.035 168.586 21.786 3319 3393 289 52 2640 7890 76 85 147 156 6.34
8 1740 2005 0 2027 311 265 286 2049 1093 833 658 918 0 791 281 260 154 722 2314 3036 1828 2550 .87 80 0 .175 .071 .476 .403 69 63 71 59 2.46 .886 .407 .378 1.992 1.129 1.05 .366 2882 2398 206 52 2790 7900 78 86 163 171 .175
9 345 576 0 370 238 231 66 364 1468 1235 1047 1280 0 941 239 233 73 647 3431 4078 2908 3556 .88 100 0 3.236 3.076 3.628 3.021 70 61 95 92 .295 .106 3.393 3.035 2.386 9.425 8.43 3.178 1599 1392 327 80 2920 7900 77 87 175 185 3.236
10 6 224 0 110 225 218 53 26 233 7 6 232 0 86 231 226 61 628 19 647 17 644 .42 100 -50 1.474 1.206 .982 30 16 25 7 3.714 1.337 .269 1 3.438 .748 2.778 .913 33 12 354 80 3080 7880 75 85 191 201 -.419
11 1216 1456 0 829 243 240 57 1110 335 92 101 344 0 122 254 243 101 675 256 931 281 956 .63 110 0 -2.119 -2.116 .125 .124 88 83 48 17 12.065 4.343 .083 .083 2.647 .23 .231 .1 1202 1317 455 80 3210 7890 75 86 203 214 -2.119
12 534 762 0 640 244 228 94 560 308 70 57 295 0 118 237 238 60 661 194 856 158 819 .65 60 0 -1.526 -1.754 .216 .21 71 59 46 31 8 2.88 .125 .107 1.91 .347 .297 .157 630 591 170 32 3370 7880 77 83 222 228 -1.526
13 500 748 0 405 264 248 69 444 304 56 63 311 0 161 261 248 69 689 156 844 175 864 .52 60 0 -1.513 -1.515 .279 .277 75 75 46 31 7.929 2.854 .126 .126 2.349 .35 .35 .217 500 563 146 32 3520 7900 79 85 237 243 -1.513
14 -4 260 0 127 311 264 323 12 242 -23 -17 248 0 93 283 265 101 736 -64 672 689 .4 100 -50 .7 .903 1 0 11 1 3.53 .157 -11 -21 432 80 3660 7880 75 85 249 259
15 1704 1949 0 2552 316 245 393 2585 568 311 181 438 0 341 320 257 514 714 864 1578 503 1217 .83 90 0 -1.581 -1.761 .171 .134 75 69 30 3 8.312 2.992 .12 .106 2.8 .334 .295 .113 2896 1885 296 52 3810 7900 77 86 264 273 -1.581
16 857 1075 0 666 234 218 76 787 361 122 129 368 0 169 240 239 69 664 339 1003 358 1022 .73 80 0 -1.216 -1.258 .251 .222 73 71 59 50 6.451 2.322 .155 .151 3.52 .431 .418 .176 909 986 248 52 3950 7900 78 86 279 287 -1.216
17 171 409 0 220 244 238 53 162 264 21 16 259 0 122 248 243 62 675 58 733 44 719 .46 60 0 -1.474 -1.944 .513 .536 71 65 43 18 7.714 2.777 .13 .094 2.254 .36 .26 .38 183 187 145 32 4110 7900 79 85 296 302 -1.474
18 34 251 0 114 234 217 89 47 461 221 16 256 0 703 369 240 670 667 614 1281 44 711 .46 100 -50 .386 1.798 1.478 30 15 10 6 .213 .077 4.702 .471 4.276 13.061 1.307 20.819 268 50 406 80 4250 7880 75 85 308 318 3.707
19 695 927 0 364 264 232 121 618 383 131 122 374 0 175 449 252 815 700 364 1064 339 1039 .14 80 0 -.764 -1.036 .271 .221 82 78 0 0 4.718 1.698 .212 .176 3.627 .589 .488 10.249 749 817 267 52 4390 7890 77 85 323 331 -.764
20 614 871 0 430 281 257 119 485 407 158 169 418 0 197 255 249 77 692 439 1131 469 1161 .78 60 0 -.144 -.387 .38 .449 75 71 62 53 3.07 1.105 .326 .275 2.072 .905 .765 .378 643 783 126 32 4540 7900 79 85 339 345 -.144

Total number of rows: 43008

Table truncated, full table size 8884 Kbytes.




Supplementary data files not provided
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