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Sample GSM6344 Query DataSets for GSM6344
Status Public on Apr 15, 2004
Title AML 63
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 63
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=750640LaserPower=3.564.65
Lot batch = shdj111
 
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
1 445 638 0 135 217 193 100 450 711 395 385 701 0 132 324 316 104 510 637 1147 621 1131 .88 50 0 .502 .481 .877 .85 100 91 100 100 1.139 .706 .878 .865 1.496 1.416 1.395 1.05 845 830 90 12 1570 8700 31 36 18 23 .502
2 1928 2093 0 963 170 165 46 2055 739 451 400 688 0 301 297 288 98 465 727 1192 645 1110 .87 70 0 -1.498 -1.579 .208 .244 100 100 90 78 4.557 2.825 .219 .207 1.634 .354 .335 .232 2506 2328 236 32 1720 8700 30 37 32 39 -1.498
3 1712 1879 0 1732 168 167 43 2338 928 723 575 780 0 512 230 205 95 331 1166 1497 927 1258 .95 60 0 -1.004 -.884 .33 .315 100 100 100 96 3.234 2.005 .309 .336 1.521 .499 .542 .28 3061 2287 176 32 1870 8710 32 38 48 54 -1.004
4 387 546 0 301 162 159 35 451 334 155 143 322 0 83 187 179 75 289 250 539 231 519 .6 60 0 -.851 -.747 .375 .389 100 100 84 43 2.91 1.804 .344 .37 2.563 .554 .596 .257 606 530 164 32 2020 8700 31 37 63 69 -.851
5 951 1111 0 639 170 160 67 1152 834 610 605 829 0 425 238 224 97 361 984 1345 976 1337 .94 60 0 -.228 .037 .439 .516 100 100 93 81 1.889 1.171 .53 .636 1.736 .854 1.026 .573 1762 1556 176 32 2160 8710 32 38 77 83 -.228
6 629 804 0 113 183 175 57 628 297 10 15 302 0 85 305 287 95 463 16 479 24 487 .08 50 0 -5.283 -4.7 .108 .117 100 100 25 0 62.8 38.936 .016 .024 1.715 .026 .038 .047 638 644 104 12 2310 8700 31 36 92 97 -5.283
7 1881 2056 0 1225 189 175 74 2014 1848 1509 1292 1631 0 933 356 339 130 547 2434 2981 2084 2631 .96 70 0 .273 .148 .766 .725 100 96 96 96 1.335 .827 .749 .687 1.565 1.208 1.108 .738 3523 3173 236 32 2460 8700 30 37 106 113 .273
8 1069 1242 0 604 189 173 73 1081 341 14 0 327 0 111 329 327 108 527 23 550 0 527 .25 60 0 -5.581 .096 .08 100 93 21 3 77.214 47.873 .013 3.336 .021 .046 1095 1069 155 32 2620 8700 31 37 123 129 -5.581
9 939 1112 0 215 198 173 104 966 536 178 170 528 0 152 361 358 117 577 287 865 274 852 .6 70 0 -1.75 -1.776 .169 .193 100 100 56 34 5.427 3.365 .184 .181 1.928 .297 .292 .218 1144 1109 218 32 2740 8700 30 37 134 141 -1.75
10 478 672 0 92 206 194 72 498 408 52 52 408 0 99 365 356 110 574 84 658 84 658 .29 50 0 -2.57 -2.511 .198 .181 100 100 25 8 9.577 5.938 .104 .109 1.98 .168 .175 .208 550 530 104 12 2890 8700 31 36 150 155 -2.57
11 8772 8946 0 3566 188 174 83 8421 815 415 350 750 0 351 403 400 130 645 669 1315 565 1210 .76 90 0 -3.653 -3.958 .048 .058 100 100 76 59 20.292 12.581 .049 .04 1.66 .079 .064 .05 8836 9122 311 52 3040 8700 29 38 163 172 -3.653
12 9477 9644 0 7984 176 167 73 11010 4960 4563 3402 3799 0 3546 401 397 126 640 7360 8000 5487 6127 .99 100 0 -.581 -.788 .393 .419 100 100 100 98 2.413 1.496 .414 .359 1.34 .668 .579 .424 15573 12879 320 80 3190 8710 30 40 178 188 -.581
13 797 963 0 418 174 166 54 903 2007 1647 1513 1873 0 957 372 360 113 581 2656 3237 2440 3021 .94 90 0 1.557 1.614 1.751 1.814 98 96 100 96 .548 .34 1.824 1.898 1.606 2.942 3.062 2.019 2550 2310 300 52 3330 8700 29 38 192 201 1.557
14 718 887 0 274 176 169 51 745 1055 716 665 1004 0 349 353 339 116 547 1155 1702 1073 1619 .92 100 0 .632 .579 .871 .952 100 100 97 90 1.041 .645 .961 .926 1.599 1.55 1.494 1.11 1461 1383 342 80 3480 8700 29 39 207 217 .632
15 1066 1236 0 380 180 170 55 1016 9235 8869 9227 9593 0 3351 379 366 154 590 14305 14895 14882 15473 .98 90 0 3.816 3.803 8.71 8.97 98 96 100 100 .115 .071 8.729 8.656 1.21 14.08 13.961 8.885 9885 10293 298 52 3620 8700 29 38 221 230 3.816
16 11882 12047 0 7639 174 165 47 12877 8337 7958 7176 7555 0 5035 399 379 143 611 12835 13447 11574 12185 .99 120 0 -.005 -.038 .584 .614 100 99 97 96 1.618 1.003 .618 .604 1.338 .997 .974 .63 20835 19058 414 120 3780 8710 29 41 236 248 -.005
17 2250 2411 0 825 170 161 46 2099 7340 6954 7532 7918 0 2737 399 386 120 623 11216 11839 12148 12771 .98 120 0 2.418 2.433 3.32 3.347 99 99 100 100 .302 .187 3.313 3.348 1.233 5.344 5.399 3.374 9053 9782 383 120 3930 8700 28 40 251 263 2.418
18 41 199 0 398 166 158 46 134 523 120 53 456 0 229 409 403 120 650 194 844 85 735 .14 100 -50 1.06 2.211 3.536 46 25 41 27 1.117 .692 .896 1.293 5.409 1.444 2.085 .212 254 94 299 80 4070 8700 29 39 266 276 .53
19 5583 5746 0 2261 166 163 43 5233 1280 906 845 1219 0 485 386 374 118 603 1461 2065 1363 1966 .95 100 0 -1.84 -2.034 .158 .165 100 100 95 91 5.776 3.581 .173 .151 1.502 .279 .244 .176 6139 6428 309 80 4220 8700 29 39 281 291 -1.84
20 2590 2748 0 997 164 158 45 2562 1419 1083 1134 1470 0 484 350 336 106 542 1747 2289 1829 2371 .95 110 0 -.553 -.502 .409 .419 100 100 98 95 2.366 1.467 .423 .438 1.338 .682 .706 .425 3645 3724 381 80 4360 8700 28 39 294 305 -.553

Total number of rows: 43008

Table truncated, full table size 8893 Kbytes.




Supplementary data files not provided
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