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Sample GSM6272 Query DataSets for GSM6272
Status Public on Apr 15, 2004
Title AML 2
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 2
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=650650LaserPower=3.984.69
Lot batch = shcz081
 
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 GPL318
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
1 323 480 0 198 172 157 145 368 322 178 164 308 0 104 148 144 43 180 223 403 205 385 .67 80 0 -.726 -.656 .474 .432 94 67 92 82 2.067 1.654 .484 .508 1.95 .605 .635 .315 546 487 280 52 1990 8050 21 29 51 59 -.726
2 3314 3474 0 2009 202 160 179 3334 8636 8488 8576 8724 0 5014 193 148 173 185 10610 10795 10720 10905 .98 90 0 1.67 1.694 2.603 2.643 100 96 100 100 .393 .314 2.546 2.588 1.351 3.182 3.235 2.561 11822 11890 340 52 2140 8050 20 29 65 74 1.67
3 2051 2207 0 923 159 156 38 2016 779 635 613 757 0 289 147 144 40 180 794 974 766 946 .96 80 0 -1.345 -1.42 .322 .326 100 100 100 98 3.175 2.54 .315 .299 1.446 .394 .374 .303 2651 2664 234 52 2290 8050 21 29 81 89 -1.345
4 634 791 0 279 160 157 37 688 1284 1137 1070 1217 0 484 147 147 39 184 1421 1605 1338 1521 .95 80 0 1.047 1.077 1.645 1.706 100 100 100 100 .605 .484 1.653 1.688 1.362 2.066 2.11 1.701 1825 1704 246 52 2430 8050 21 29 95 103 1.047
5 335 485 0 240 156 150 37 357 320 182 175 313 0 94 141 138 38 173 228 400 219 391 .81 100 0 -.65 -.615 .577 .565 93 91 95 87 1.962 1.569 .51 .522 1.824 .637 .653 .421 539 510 361 80 2580 8050 20 30 109 119 -.65
6 472 626 0 207 155 154 39 483 242 106 111 247 0 57 138 136 34 170 133 303 139 309 .7 60 0 -1.866 -1.766 .219 .248 100 96 93 68 4.557 3.645 .219 .235 1.883 .274 .294 .187 589 583 158 32 2730 8050 22 28 126 132 -1.866
7 573 726 0 357 155 153 33 607 1131 999 908 1040 0 519 134 132 32 165 1249 1414 1135 1300 .94 90 0 1.041 .986 1.701 1.716 100 100 100 100 .608 .486 1.646 1.585 1.456 2.057 1.981 1.596 1606 1481 332 52 2870 8050 20 29 138 147 1.041
8 384 546 0 132 172 162 56 390 183 42 35 176 0 43 140 141 33 176 53 229 44 220 .35 70 0 -2.893 -3.134 .108 .094 100 100 53 25 9.286 7.429 .108 .091 2.338 .135 .114 .088 432 419 206 32 3010 8050 21 28 153 160 -2.893
9 88 248 0 66 165 160 50 96 317 181 167 303 0 101 141 136 35 170 226 396 209 379 .54 80 0 1.237 1.246 1.785 1.636 73 42 98 86 .53 .424 1.885 1.898 2.415 2.357 2.372 2.371 277 255 274 52 3170 8050 21 29 169 177 1.237
10 388 549 0 102 164 161 40 395 182 42 46 186 0 46 141 140 35 175 53 228 58 233 .41 80 0 -2.911 -2.754 .112 .129 100 100 53 23 9.405 7.524 .106 .119 2.266 .133 .148 .107 437 434 266 52 3310 8050 21 29 183 191 -2.911
11 1057 1214 0 336 161 157 37 1009 208 75 76 209 0 50 135 133 34 166 94 260 95 261 .54 70 0 -3.428 -3.476 .077 .08 100 100 81 56 13.453 10.763 .074 .072 1.843 .093 .09 .062 1084 1133 212 32 3460 8050 21 28 198 205 -3.428
12 1722 1874 0 764 154 152 34 1574 1210 1076 1151 1285 0 518 137 134 35 168 1345 1513 1439 1606 .96 80 0 -.227 -.259 .702 .71 100 100 100 100 1.463 1.17 .684 .668 1.407 .855 .836 .663 2650 2873 277 52 3600 8060 22 30 212 220 -.227
13 566 720 0 373 155 154 34 564 417 281 259 395 0 130 137 136 34 170 351 521 324 494 .87 80 0 -.683 -.806 .569 .523 92 92 100 96 2.007 1.606 .498 .458 1.962 .623 .572 .409 845 825 262 52 3750 8060 22 30 227 235 -.683
14 100 254 0 53 157 154 36 111 190 60 49 179 0 45 137 130 38 163 75 238 61 224 .41 70 0 -.566 -.707 .529 .575 93 78 65 31 1.85 1.48 .541 .49 2.169 .676 .613 .475 171 149 198 32 3900 8060 22 29 242 249 -.566
15 1043 1201 0 421 159 158 38 1000 464 327 340 477 0 104 140 137 37 171 409 580 425 596 .9 90 0 -1.291 -1.295 .345 .323 100 100 100 98 3.058 2.446 .327 .326 1.548 .409 .407 .284 1327 1383 317 52 4040 8060 21 30 255 264 -1.291
16 2923 3082 0 2207 161 159 36 2967 4530 4396 4306 4440 0 3161 137 134 37 168 5495 5663 5383 5550 .98 100 0 .889 .881 1.586 1.522 100 98 100 100 .675 .54 1.482 1.473 1.444 1.852 1.841 1.466 7363 7229 355 80 4190 8070 22 32 270 280 .889
17 896 1055 0 568 161 159 37 886 4070 3935 4226 4361 0 2272 136 135 34 169 4919 5088 5283 5451 .97 100 0 2.473 2.56 5.012 4.561 97 93 100 100 .225 .18 4.441 4.717 1.629 5.552 5.896 4.397 4821 5122 384 80 4340 8060 21 31 285 295 2.473
18 128 282 0 66 156 154 34 137 162 24 17 155 0 41 138 138 37 173 30 203 21 194 .27 60 0 -2.191 -2.591 .231 .21 96 84 25 12 5.708 4.567 .175 .133 3.009 .219 .166 .175 161 145 165 32 4490 8070 24 30 302 308 -2.191
19 660 820 0 353 163 160 39 754 367 223 224 368 0 96 144 144 33 180 279 459 280 460 .87 60 0 -1.436 -1.237 .296 .292 100 100 100 90 3.381 2.705 .296 .339 1.691 .37 .424 .269 977 884 170 32 4640 8060 23 29 317 323 -1.436
20 680 840 0 290 163 160 38 640 623 478 498 643 0 187 149 145 42 181 598 779 623 804 .92 70 0 -.099 -.127 .795 .81 100 93 100 100 1.339 1.071 .747 .732 1.443 .934 .915 .694 1118 1178 206 32 4780 8060 22 29 330 337 -.099

Total number of rows: 43008

Table truncated, full table size 8999 Kbytes.




Supplementary data files not provided
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