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Sample GSM6345 Query DataSets for GSM6345
Status Public on Apr 15, 2004
Title AML 52
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 52
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix Pro
Software version: 3.0.6.81
Scanning parameters: PMTVolts=690650LaserPower=3.574.65
Lot batch = shdj112
 
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
1 601 760 0 189 165 159 43 571 361 180 152 333 0 103 194 181 71 245 243 488 205 450 .58 70 0 -1.231 -1.549 .291 .271 100 100 87 59 3.172 2.347 .315 .253 1.58 .426 .342 .276 751 753 205 32 1650 8660 18 25 21 28 -1.231
2 1869 2025 0 773 162 156 41 1972 500 321 298 477 0 171 182 179 59 242 434 676 403 645 .82 80 0 -2.185 -2.214 .149 .17 100 100 96 88 6.143 4.546 .163 .159 1.799 .22 .215 .148 2293 2167 287 52 1800 8650 17 25 36 44 -2.185
3 1982 2143 0 1807 164 161 37 2472 898 714 580 764 0 446 191 184 69 249 965 1214 784 1032 .89 70 0 -1.357 -1.338 .315 .299 100 100 96 93 3.462 2.562 .289 .293 2.104 .39 .395 .24 3186 2562 220 32 1950 8650 17 24 51 58 -1.357
4 529 691 0 267 171 162 99 527 319 124 129 324 0 118 209 195 76 264 168 431 174 438 .55 70 0 -1.653 -1.601 .22 .258 96 90 68 43 4.25 3.145 .235 .244 2.588 .318 .33 .178 651 658 214 32 2090 8650 17 24 65 72 -1.653
5 1994 2158 0 1133 168 164 41 2092 1775 1583 1434 1626 0 910 200 192 80 259 2139 2399 1938 2197 .92 90 0 .032 -.041 .766 .826 100 100 100 100 1.322 .978 .757 .719 1.74 1.023 .972 .751 3675 3428 325 52 2250 8660 17 26 80 89 .032
6 650 815 0 197 166 165 38 603 320 136 146 330 0 97 195 184 65 249 184 432 197 446 .55 70 0 -1.714 -1.72 .213 .232 100 100 75 62 4.434 3.281 .226 .225 2.253 .305 .304 .197 739 796 192 32 2390 8650 17 24 95 102 -1.714
7 1294 1459 0 1270 169 165 40 1621 1775 1590 1582 1767 0 1202 193 185 61 250 2149 2399 2138 2388 .87 80 -100 .724 1.006 1.024 96 92 96 92 1.019 .754 .981 1.223 1.996 1.326 1.652 .97 3211 2876 268 52 2520 8660 18 26 108 116 .407
8 1281 1444 0 553 166 163 39 1313 332 140 146 338 0 97 199 192 64 259 189 449 197 457 .63 80 0 -2.795 -2.699 .11 .109 100 100 73 57 9.379 6.94 .107 .114 1.941 .144 .154 .098 1453 1427 273 52 2680 8650 17 25 124 132 -2.795
9 988 1153 0 315 172 165 70 1006 480 280 263 463 0 153 213 200 74 270 378 649 355 626 .83 100 0 -1.411 -1.475 .257 .274 100 100 93 80 3.593 2.659 .278 .266 1.636 .376 .36 .267 1286 1251 373 80 2830 8650 16 26 138 148 -1.411
10 642 809 0 200 171 167 41 660 403 199 203 407 0 111 216 204 70 276 269 545 274 550 .69 70 0 -1.295 -1.227 .264 .301 100 100 93 53 3.317 2.454 .302 .316 1.727 .407 .427 .299 859 845 176 32 2970 8660 18 25 153 160 -1.295
11 11250 11413 0 3956 165 163 39 10637 1086 894 843 1035 0 491 199 192 65 259 1208 1468 1139 1399 .93 100 0 -3.138 -3.304 .078 .09 100 100 93 91 11.898 8.805 .084 .075 1.566 .114 .101 .085 11531 12093 352 80 3110 8660 17 27 166 176 -3.138
12 14565 14728 0 7654 281 163 1519 15417 8395 8212 7786 7969 0 4974 321 183 1288 247 11097 11345 10522 10769 .95 100 0 -.474 -.469 .442 .549 97 97 90 87 1.877 1.389 .533 .535 1.937 .72 .722 .551 23629 22351 362 80 3260 8650 16 26 181 191 -.474
13 1224 1379 0 538 156 155 67 1256 535 355 359 539 0 189 185 180 58 243 480 723 485 728 .85 100 0 -1.389 -1.335 .265 .276 100 100 95 86 3.538 2.618 .283 .293 1.882 .382 .396 .266 1611 1583 351 80 3410 8650 16 26 196 206 -1.389
14 747 897 0 390 146 150 65 784 757 599 634 792 0 299 167 158 66 214 809 1023 857 1070 .87 100 0 .046 .198 .749 .844 96 95 91 87 1.309 .969 .764 .849 1.76 1.032 1.147 .751 1383 1381 356 80 3550 8660 17 27 210 220 .046
15 2229 2385 0 2636 153 156 59 2070 703 542 590 751 0 597 169 161 69 218 732 950 797 1015 .83 100 -100 -1.483 .423 .359 63 62 60 57 3.819 2.826 .262 .265 2.36 .354 .358 .201 2612 2819 346 80 3700 8660 17 27 225 235 -1.499
16 18912 19074 0 3827 160 162 39 17909 25189 25008 25383 25564 0 5346 188 181 64 245 33795 34039 34301 34546 .97 110 0 .916 .859 1.396 1.431 100 100 100 100 .716 .53 1.396 1.342 1.232 1.887 1.814 1.399 42917 44295 396 80 3850 8650 15 26 239 250 .916
17 2152 2310 0 963 160 158 36 1999 7093 6906 6911 7098 0 3443 193 187 63 253 9332 9585 9339 9592 .96 120 0 2.223 2.118 3.482 3.559 97 96 98 98 .289 .214 3.455 3.211 1.567 4.669 4.34 3.617 8905 9063 416 120 4000 8660 16 28 254 266 2.223
18 40 194 0 216 157 154 34 107 262 70 39 231 0 149 198 192 61 259 95 354 53 312 .61 100 -50 .398 1.075 1.126 56 35 40 18 1.529 1.131 .654 .975 3.972 .884 1.318 .675 177 79 309 80 4140 8650 16 26 269 279 -.178
19 6576 6734 0 1356 160 158 40 6515 2722 2529 2635 2828 0 748 200 193 65 261 3418 3678 3561 3822 .96 110 0 -.931 -.885 .375 .383 100 100 100 100 2.576 1.906 .388 .401 1.337 .525 .541 .393 9044 9211 366 80 4290 8650 15 26 283 294 -.931
20 3400 3561 0 741 166 161 43 3331 2577 2385 2545 2737 0 753 199 192 72 259 3223 3482 3439 3699 .96 110 0 -.048 .017 .639 .743 100 100 98 97 1.397 1.034 .716 .749 1.851 .968 1.012 .737 5716 5945 417 80 4430 8650 15 26 297 308 -.048

Total number of rows: 43008

Table truncated, full table size 9105 Kbytes.




Supplementary data files not provided
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