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Sample GSM6296 Query DataSets for GSM6296
Status Public on Apr 15, 2004
Title AML 80
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 80
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=780630LaserPower=3.574.71
Lot batch = shcz105
 
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
1 402 575 0 203 178 173 34 404 394 114 81 361 0 151 282 280 96 459 187 646 133 592 .4 60 0 -1.112 -1.598 .332 .362 96 96 43 25 3.544 2.162 .282 .201 2.674 .463 .33 .395 518 483 160 32 1680 8120 37 43 17 23 -1.112
2 1403 1584 0 585 184 181 44 1354 521 248 178 451 0 188 280 273 96 448 407 854 292 739 .68 60 0 -1.736 -2.265 .175 .169 100 100 78 46 5.46 3.33 .183 .127 1.876 .3 .208 .189 1602 1581 172 32 1820 8120 37 43 31 37 -1.736
3 5440 5634 0 2483 219 194 88 5088 1515 1247 1276 1544 0 606 288 268 104 439 2044 2484 2092 2531 .93 60 0 -1.316 -1.379 .245 .261 100 100 100 93 4.08 2.489 .245 .235 1.614 .402 .385 .22 6335 6716 176 32 1960 8120 37 43 45 51 -1.316
4 404 584 0 215 193 180 61 385 628 336 265 557 0 274 297 292 96 479 551 1030 434 913 .76 70 0 .517 .105 .718 .921 93 90 84 65 1.146 .699 .873 .656 2.374 1.431 1.075 1.154 721 669 236 32 2110 8120 36 43 59 66 .517
5 427 602 0 550 183 175 52 617 737 468 371 640 0 370 275 269 92 441 767 1208 608 1049 .88 90 0 .314 .51 .898 .691 88 82 84 75 1.318 .804 .759 .869 2.523 1.243 1.424 .731 1085 798 341 52 2270 8110 34 43 74 83 .314
6 405 581 0 201 180 176 45 388 393 133 119 379 0 134 277 260 104 426 218 644 195 621 .37 60 0 -.832 -1.054 .321 .409 93 93 59 31 2.917 1.78 .343 .294 3.583 .562 .482 .321 521 524 165 32 2410 8120 37 43 90 96 -.832
7 483 654 0 599 173 171 38 678 914 640 532 806 0 589 278 274 98 449 1049 1498 872 1321 .94 80 0 .63 .853 1.017 .964 90 84 86 75 1.059 .646 .944 1.101 1.97 1.547 1.806 .978 1318 1015 268 52 2550 8120 36 44 103 111 .63
8 426 601 0 389 180 175 45 497 385 119 115 381 0 143 271 266 88 436 195 631 189 625 .51 80 0 -1.349 -1.176 .269 .299 84 80 55 32 4.176 2.548 .239 .27 2.985 .393 .443 .232 616 541 278 52 2690 8130 37 45 117 125 -1.349
9 915 1092 0 570 182 177 39 975 950 688 705 967 0 312 277 262 93 430 1128 1557 1156 1585 .87 60 0 .21 .337 .778 .734 93 93 96 93 1.417 .864 .706 .77 1.728 1.157 1.263 .612 1663 1620 171 32 2840 8120 37 43 133 139 .21
10 372 547 0 243 182 175 45 404 420 149 153 424 0 160 280 271 94 444 244 689 251 695 .51 90 0 -.726 -.569 .457 .503 90 90 61 40 2.711 1.654 .369 .411 2.355 .605 .674 .461 553 525 344 52 2990 8120 35 44 146 155 -.726
11 3950 4134 0 2057 192 184 47 4129 1222 950 983 1255 0 515 271 272 87 446 1557 2003 1611 2057 .95 70 0 -1.407 -1.293 .232 .221 100 100 100 96 4.346 2.651 .23 .249 1.593 .377 .408 .228 5079 4933 218 32 3130 8120 36 43 161 168 -1.407
12 3140 3318 0 3412 185 178 51 3786 2090 1821 1371 1640 0 1661 277 269 97 441 2985 3426 2248 2689 .98 80 0 -.343 -.482 .521 .491 100 98 96 86 2.079 1.268 .481 .437 1.704 .788 .716 .477 5607 4511 297 52 3280 8120 36 44 176 184 -.343
13 910 1084 0 404 183 174 45 932 650 374 320 596 0 218 285 276 106 452 613 1066 525 977 .73 70 0 -.604 -.795 .391 .408 100 96 93 78 2.492 1.52 .401 .352 1.833 .658 .576 .407 1306 1230 216 32 3430 8110 35 42 191 198 -.604
14 333 510 0 304 179 177 36 422 622 341 327 608 0 214 285 281 101 461 559 1020 536 997 .72 70 0 .406 .687 .874 .728 90 90 90 62 1.238 .755 .808 .982 2.749 1.325 1.61 .81 763 660 223 32 3570 8120 36 43 205 212 .406
15 2621 2798 0 1449 183 177 46 2505 1899 1627 1752 2024 0 999 278 272 89 446 2667 3113 2872 3318 .96 80 0 .091 .132 .634 .644 98 98 98 94 1.54 .939 .65 .668 1.71 1.065 1.096 .65 4132 4373 277 52 3720 8110 35 43 220 228 .091
16 13780 13954 0 7191 199 174 116 12179 16672 16391 17840 18121 0 9435 309 281 164 461 26870 27331 29246 29707 .99 90 0 1.142 1.086 1.379 1.357 100 100 100 100 .743 .453 1.346 1.295 1.86 2.206 2.122 1.337 28570 31620 317 52 3860 8120 35 44 233 242 1.142
17 1179 1351 0 571 195 172 112 1137 2573 2292 2347 2628 0 1168 305 281 151 461 3757 4218 3848 4308 .97 90 0 1.724 1.706 1.945 2.001 96 92 96 92 .496 .303 2.016 1.991 1.661 3.305 3.263 2.055 3429 3526 316 52 4010 8120 35 44 248 257 1.724
18 838 1007 0 404 171 169 30 808 421 151 129 399 0 154 278 270 81 443 248 690 211 654 .43 70 0 -1.707 -1.986 .183 .216 93 93 62 46 5.351 3.264 .187 .154 2.934 .306 .252 .174 959 967 212 32 4150 8120 36 43 263 270 -1.707
19 1866 2038 0 1291 174 172 38 1972 1027 758 608 877 0 540 279 269 95 441 1243 1684 997 1438 .92 70 0 -.666 -.905 .387 .394 100 100 93 87 2.602 1.587 .384 .326 1.938 .63 .534 .378 2730 2474 225 32 4300 8110 35 42 278 285 -.666
20 2060 2233 0 997 181 173 58 2086 1501 1233 1191 1459 0 783 277 268 102 439 2021 2461 1952 2392 .95 70 0 -.045 -.077 .516 .551 100 100 100 93 1.692 1.032 .591 .578 1.447 .969 .948 .625 3319 3251 218 32 4450 8110 35 42 293 300 -.045

Total number of rows: 43008

Table truncated, full table size 9615 Kbytes.




Supplementary data files not provided
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