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Sample GSM6233 Query DataSets for GSM6233
Status Public on Apr 15, 2004
Title AML 19
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 19
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=670650LaserPower=4.144.43
Lot batch = shco024
 
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
1 201 413 0 114 216 212 54 201 309 113 121 317 0 42 206 196 64 276 159 435 170 446 .33 50 0 -.337 -.238 .63 .629 91 66 91 33 1.779 1.263 .562 .602 1.567 .792 .848 .382 314 322 90 12 1790 7050 78 83 56 61 -.337
2 264 464 0 211 209 200 47 254 273 83 88 278 0 83 195 190 50 268 117 385 124 392 .54 70 0 -1.12 -1.091 .361 .386 81 75 65 37 3.06 2.173 .327 .333 2.862 .46 .469 .271 337 352 176 32 1950 7050 77 84 71 78 -1.12
3 1361 1579 0 741 249 218 184 1345 337 135 132 334 0 115 213 202 72 285 190 475 186 470 .71 80 0 -2.822 -2.872 .106 .099 94 88 65 48 9.963 7.074 .1 .097 2.22 .141 .137 .093 1480 1493 214 52 2060 7060 78 86 82 90 -2.822
4 2574 2800 0 2253 253 226 146 2866 1626 1427 1148 1347 0 1036 210 199 81 280 2010 2290 1617 1897 .98 90 0 -.512 -.671 .532 .502 88 86 98 94 2.008 1.426 .498 .446 1.476 .701 .628 .466 4293 3722 285 52 2230 7070 78 87 98 107 -.512
5 617 849 0 287 257 232 80 634 348 169 148 327 0 109 190 179 50 252 238 490 208 461 .8 50 0 -1.413 -1.566 .26 .239 100 100 83 83 3.751 2.664 .267 .24 1.402 .375 .338 .256 803 765 104 12 2370 7050 78 83 114 119 -1.413
6 193 406 0 81 215 213 48 199 311 131 133 313 0 80 189 180 47 254 185 438 187 441 .52 50 0 -.109 -.043 .663 .667 100 91 91 75 1.519 1.079 .658 .689 1.883 .927 .971 .505 330 326 99 12 2540 7050 78 83 131 136 -.109
7 492 724 0 407 249 232 87 503 511 331 339 519 0 220 194 180 64 254 466 720 477 731 .88 70 0 -.11 -.043 .593 .611 78 75 81 78 1.52 1.079 .658 .689 1.87 .927 .97 .591 834 831 216 32 2680 7050 77 84 144 151 -.11
8 2548 2756 0 2232 217 208 64 2850 2079 1913 1674 1840 0 1366 181 166 97 234 2694 2928 2358 2592 .97 90 0 -.081 -.112 .846 .667 92 90 96 94 1.49 1.058 .671 .657 2.153 .945 .925 .632 4763 4222 270 52 2810 7040 75 84 156 165 -.081
9 551 759 0 379 212 208 42 586 1001 831 843 1013 0 493 176 170 65 239 1170 1410 1187 1427 .94 100 0 .998 1.108 1.357 1.396 88 87 98 90 .705 .501 1.418 1.53 1.646 1.997 2.155 1.39 1417 1394 362 80 2950 7050 76 86 170 180 .998
10 18 231 0 138 275 213 315 66 206 36 25 195 0 62 194 170 113 239 51 290 35 275 .42 100 -50 .968 .66 .674 8 0 10 1 1.833 1.302 .545 1.389 2.98 .768 1.956 .354 102 43 385 80 3110 7030 74 84 186 196 -.38
11 1490 1695 0 826 220 205 124 1353 768 599 578 747 0 357 178 169 64 238 844 1082 814 1052 .94 110 0 -.681 -.872 .47 .457 96 82 96 90 2.259 1.604 .443 .388 1.597 .624 .546 .41 1952 2068 437 80 3240 7040 74 85 198 209 -.681
12 355 555 0 446 207 200 54 479 508 329 210 389 0 280 179 179 47 252 463 715 296 548 .9 80 0 -.048 -.263 .678 .658 84 76 92 80 1.456 1.034 .687 .592 1.875 .967 .833 .634 808 565 291 52 3410 7030 75 83 217 225 -.048
13 490 691 0 321 208 201 56 515 322 147 151 326 0 88 181 175 46 246 207 454 213 459 .73 70 0 -1.315 -1.204 .318 .29 90 87 87 81 3.503 2.487 .285 .308 1.723 .402 .434 .258 662 641 185 32 3550 7050 77 84 231 238 -1.315
14 9 203 0 105 197 194 48 37 205 34 32 203 0 62 183 171 112 241 48 289 45 286 .27 100 -50 2.324 .776 .8 38 17 8 1 1.088 .773 .919 3.556 3.293 1.294 5.008 .428 71 41 342 80 3700 7030 74 84 245 255 .372
15 2931 3120 0 2434 196 189 69 3233 808 638 520 690 0 502 174 170 52 239 899 1138 732 972 .95 110 0 -1.847 -2.001 .207 .191 96 96 96 96 5.067 3.598 .197 .177 1.735 .278 .25 .191 3871 3451 341 80 3830 7040 74 85 257 268 -1.847
16 661 860 0 556 230 199 158 677 423 249 206 380 0 196 185 174 78 245 351 596 290 535 .88 90 0 -.949 -1.188 .485 .416 76 63 75 61 2.719 1.93 .368 .312 3.223 .518 .439 .342 926 867 321 52 3980 7020 73 82 273 282 -.949
17 35 242 0 141 219 207 97 92 194 23 21 192 0 57 177 171 53 241 32 273 30 270 .29 100 -50 -.243 .533 .419 35 23 23 10 4 2.84 .25 .6 3.957 .352 .845 .205 115 56 364 80 4140 7030 74 84 289 299 -1.506
18 24 227 0 86 208 203 42 37 186 19 18 185 0 55 171 167 43 235 27 262 25 261 .17 100 -50 .079 .71 .758 42 18 27 10 1.947 1.383 .514 .75 3.592 .723 1.056 .373 56 42 301 80 4280 7030 74 84 303 313 -.467
19 801 1006 0 394 211 205 51 812 610 435 424 599 0 190 178 175 48 246 613 859 597 844 .91 110 0 -.406 -.424 .559 .538 97 97 98 97 1.867 1.325 .536 .529 1.469 .755 .746 .486 1247 1225 419 80 4420 7030 73 84 316 327 -.406
20 329 529 0 278 212 200 62 362 451 276 274 449 0 168 181 175 59 246 389 635 386 632 .86 80 0 .103 .23 .763 .73 86 78 88 80 1.312 .931 .762 .833 1.798 1.074 1.173 .684 638 603 235 52 4580 7020 74 82 334 342 .103

Total number of rows: 43008

Table truncated, full table size 9134 Kbytes.




Supplementary data files not provided
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