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Sample GSM6316 Query DataSets for GSM6316
Status Public on Apr 15, 2004
Title AML 119
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 119
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=690650LaserPower=3.914.52
Lot batch = shdj083
 
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 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 �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
1 150 283 0 252 149 133 70 237 297 159 113 251 0 169 153 138 73 131 151 283 108 239 .83 120 0 -.646 -.479 .778 .754 60 51 60 45 1.491 1.565 .671 .753 2.511 .639 .717 .66 396 263 587 120 1820 8340 16 28 20 32 -.646
2 4450 4586 0 2088 144 136 45 4442 6433 6293 6236 6376 0 3228 151 140 60 133 5993 6127 5939 6072 .98 90 0 .432 .416 1.379 1.384 100 100 100 100 .706 .741 1.417 1.401 1.377 1.349 1.335 1.468 10735 10686 318 52 1980 8360 19 28 37 46 .432
3 1426 1556 0 895 136 130 34 1421 1341 1201 1025 1165 0 788 146 140 48 133 1144 1277 976 1110 .95 70 0 -.313 -.547 .868 .905 100 100 100 100 1.183 1.242 .845 .719 1.443 .805 .685 .85 2622 2451 219 32 2140 8360 20 27 54 61 -.313
4 723 859 0 437 135 136 30 714 575 440 394 529 0 276 140 135 46 129 419 548 375 504 .91 80 0 -.769 -.946 .604 .613 98 94 96 92 1.623 1.704 .616 .545 2.002 .587 .519 .592 1154 1117 249 52 2280 8350 19 27 68 76 -.769
5 1452 1588 0 819 139 136 35 1500 2288 2152 1983 2119 0 1197 141 136 47 130 2050 2179 1889 2018 .95 90 0 .45 .379 1.448 1.413 100 100 100 100 .697 .732 1.435 1.366 1.478 1.366 1.301 1.462 3652 3435 296 52 2420 8350 18 27 81 90 .45
6 955 1091 0 384 138 136 34 974 1502 1359 1397 1540 0 642 144 143 44 136 1294 1430 1330 1467 .96 70 0 .41 .478 1.325 1.446 100 100 100 100 .717 .753 1.395 1.463 1.314 1.329 1.393 1.464 2333 2352 213 32 2560 8350 19 26 96 103 .41
7 1463 1607 0 1021 146 144 32 1602 3418 3278 2911 3051 0 1778 141 140 44 133 3122 3255 2772 2906 .96 80 0 .963 .922 2.359 2.059 100 100 100 100 .489 .513 2.046 1.99 1.682 1.949 1.895 1.98 4880 4374 276 52 2720 8360 20 28 112 120 .963
8 899 1039 0 341 151 140 64 912 515 371 327 471 0 233 147 144 47 137 353 490 311 449 .87 70 0 -1.368 -1.529 .355 .404 100 100 93 90 2.458 2.581 .407 .364 1.84 .387 .346 .426 1283 1226 200 32 2850 8350 19 26 125 132 -1.368
9 594 735 0 204 148 141 55 550 1446 1307 1368 1507 0 452 144 139 47 132 1245 1377 1303 1435 .93 90 0 1.178 1.133 2.464 2.315 98 96 100 100 .421 .442 2.376 2.303 1.482 2.263 2.193 2.545 1857 1962 347 52 3000 8360 19 28 139 148 1.178
10 377 515 0 203 142 138 34 403 387 236 198 349 0 132 154 151 44 144 225 369 189 332 .84 60 0 -.842 -.999 .538 .574 100 100 96 87 1.708 1.793 .586 .525 2.102 .558 .5 .564 639 575 158 32 3160 8350 20 26 157 163 -.842
11 4643 4783 0 1760 144 140 30 4459 846 703 663 806 0 361 148 143 46 136 670 806 631 768 .94 100 0 -2.736 -2.878 .146 .159 100 100 98 96 6.343 6.66 .158 .143 1.65 .15 .136 .157 5162 5306 369 80 3300 8360 19 29 169 179 -2.736
12 6220 6361 0 4274 147 141 33 6728 12322 12181 10595 10736 0 8043 146 141 49 134 11601 11735 10090 10225 .98 100 0 .786 .698 1.794 1.752 100 100 100 100 .552 .58 1.81 1.703 1.376 1.724 1.622 1.856 18909 16815 346 80 3450 8360 19 29 184 194 .786
13 906 1046 0 423 146 140 32 1012 1617 1477 1354 1494 0 661 145 140 48 133 1407 1540 1290 1423 .94 100 0 .475 .509 1.44 1.416 100 100 100 100 .685 .719 1.459 1.494 1.403 1.39 1.423 1.501 2489 2260 315 80 3590 8360 19 29 198 208 .475
14 302 442 0 102 145 140 36 329 532 397 388 523 0 133 142 135 46 129 378 507 370 498 .88 110 0 .201 .291 1.189 1.16 100 100 100 100 .829 .87 1.207 1.285 1.434 1.149 1.224 1.287 726 690 385 80 3730 8360 18 29 211 222 .201
15 1014 1156 0 442 145 142 29 989 5708 5567 5761 5902 0 2449 146 141 48 134 5302 5436 5487 5621 .98 100 0 2.422 2.436 5.712 5.52 100 100 100 100 .178 .187 5.629 5.681 1.365 5.361 5.411 5.708 6556 6775 326 80 3880 8360 19 29 227 237 2.422
16 6262 6407 0 2318 146 145 29 6415 18365 18215 18249 18399 0 6354 154 150 52 143 17348 17490 17380 17523 .98 110 0 1.435 1.473 2.845 2.841 100 100 100 100 .352 .37 2.839 2.914 1.241 2.704 2.775 2.863 24630 24511 362 80 4020 8360 18 29 240 251 1.435
17 1993 2135 0 697 144 142 35 1812 27094 26948 29552 29698 0 9895 152 146 49 139 25665 25804 28145 28284 .98 120 0 3.824 3.82 15.063 15.109 100 100 100 100 .067 .071 14.872 14.828 1.317 14.164 14.122 14.942 28760 31545 421 120 4170 8360 18 30 255 267 3.824
18 18 159 0 143 140 141 31 60 215 74 23 164 0 136 148 141 43 134 70 205 22 156 .71 100 -50 .283 1.324 1.099 40 22 41 30 .811 .851 1.233 1.278 4.294 1.175 1.217 1.073 134 41 301 80 4320 8350 18 28 271 281 .232
19 4154 4301 0 1409 346 147 1240 4055 2257 2112 2248 2393 0 787 320 145 1079 138 2011 2150 2141 2279 .98 110 0 -1.011 -.956 .508 .517 100 81 88 52 1.92 2.016 .521 .541 1.334 .496 .515 .516 6167 6402 331 80 4460 8360 18 29 284 295 -1.011
20 2428 2568 0 630 160 140 160 2289 2580 2436 2522 2666 0 674 169 144 269 137 2320 2457 2402 2539 .98 110 0 .019 -.016 1.067 1.075 100 100 100 100 .94 .987 1.064 1.039 1.188 1.014 .989 1.07 4725 4950 364 80 4600 8360 18 29 298 309 .019

Total number of rows: 43008

Table truncated, full table size 9559 Kbytes.




Supplementary data files not provided
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