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Sample GSM6335 Query DataSets for GSM6335
Status Public on Apr 15, 2004
Title AML 16
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 16
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=750640LaserPower=4.664.43
Lot batch = shdj102
 
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 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 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
1 646 777 0 209 131 131 30 655 485 281 272 476 0 161 207 204 69 352 484 836 469 821 .78 60 0 -.435 -.462 .418 .406 100 100 93 84 2.331 1.352 .429 .421 1.604 .74 .726 .447 936 918 165 32 1500 8490 22 28 15 21 -.435
2 5703 5831 0 2569 128 128 28 5675 2692 2493 2354 2553 0 1281 205 199 68 343 4298 4641 4059 4402 .98 90 0 -.401 -.491 .427 .438 100 100 100 100 2.276 1.32 .439 .413 1.311 .757 .712 .443 8168 8057 328 52 1640 8500 21 30 27 36 -.401
3 1085 1214 0 1156 131 129 28 1506 1044 835 618 827 0 688 213 209 71 360 1440 1800 1066 1426 .93 60 0 -.065 -.026 .525 .566 100 100 93 90 1.804 1.046 .554 .57 2.002 .956 .982 .552 2341 1703 171 32 1790 8500 23 29 44 50 -.065
4 620 746 0 520 128 126 28 733 1240 1028 907 1119 0 634 208 212 70 366 1772 2138 1564 1929 .91 70 0 1.274 1.335 1.616 1.352 100 93 96 96 .713 .414 1.402 1.463 1.794 2.418 2.522 1.396 1761 1527 196 32 1940 8500 22 29 58 65 1.274
5 1626 1755 0 969 167 129 211 1703 1170 967 894 1097 0 572 224 203 129 350 1667 2017 1541 1891 .95 60 0 -.031 -.077 .509 .534 100 93 96 90 1.761 1.021 .568 .55 1.77 .979 .948 .564 2670 2520 167 32 2070 8490 22 28 72 78 -.031
6 1110 1234 0 712 143 124 123 1268 752 561 503 694 0 344 214 191 102 329 967 1297 867 1197 .9 70 0 -.391 -.356 .482 .476 96 93 96 87 2.26 1.311 .442 .453 1.822 .763 .781 .412 1829 1613 224 32 2220 8500 22 29 86 93 -.391
7 951 1076 0 1081 125 125 28 1295 1239 1042 932 1129 0 845 205 197 71 340 1797 2136 1607 1947 .96 80 0 .472 .757 .829 .811 98 96 92 90 1.243 .721 .805 .98 1.705 1.387 1.69 .784 2337 1883 264 52 2380 8500 22 30 102 110 .472
8 994 1121 0 404 136 127 49 928 386 181 135 340 0 154 208 205 70 353 312 666 233 586 .64 70 0 -1.572 -2.094 .179 .152 100 100 75 50 5.127 2.974 .195 .136 2.053 .336 .234 .19 1109 1129 210 32 2510 8490 21 28 115 122 -1.572
9 686 811 0 283 130 125 40 681 609 399 432 642 0 246 206 210 73 362 688 1050 745 1107 .87 80 0 .015 .119 .521 .572 98 96 90 84 1.707 .99 .586 .63 1.924 1.01 1.086 .632 1080 1118 284 52 2660 8490 21 29 130 138 .015
10 416 542 0 171 129 126 29 417 431 225 193 399 0 155 212 206 72 355 388 743 333 688 .68 60 0 -.104 -.322 .5 .562 96 96 84 71 1.853 1.075 .54 .464 2.354 .93 .8 .594 642 609 164 32 2810 8490 22 28 146 152 -.104
11 7635 7762 0 2663 130 127 29 6805 1052 846 820 1026 0 409 211 206 70 355 1459 1814 1414 1769 .91 90 0 -2.222 -2.433 .121 .127 100 100 96 92 8.044 4.665 .124 .107 1.577 .214 .185 .119 7651 8455 306 52 2950 8490 20 29 158 167 -2.222
12 9573 9700 0 6869 135 127 89 9893 5282 5075 4895 5102 0 3724 209 207 71 357 8750 9107 8440 8797 .99 100 0 -.177 -.182 .463 .512 100 98 98 97 1.949 1.131 .513 .511 1.522 .884 .882 .52 14968 14468 345 80 3100 8500 21 31 173 183 -.177
13 1128 1256 0 722 136 128 93 1246 3365 3160 2605 2810 0 2291 207 205 75 353 5448 5802 4491 4845 .93 100 0 2.128 1.993 2.218 2.549 97 93 98 98 .394 .229 2.536 2.309 1.901 4.373 3.982 2.919 4406 3733 311 80 3250 8500 21 31 188 198 2.128
14 682 813 0 428 134 131 35 736 1337 1132 1038 1243 0 503 208 205 75 353 1952 2305 1790 2143 .87 120 0 1.407 1.392 1.753 1.468 99 96 100 98 .65 .377 1.538 1.522 1.924 2.652 2.624 1.502 1868 1720 451 120 3400 8490 19 31 202 214 1.407
15 685 816 0 372 136 131 31 653 18392 18185 17954 18161 0 9452 211 207 72 357 31353 31710 30955 31312 .97 110 0 5.585 5.498 29.101 27.689 95 93 100 100 .036 .021 27.848 26.21 1.395 48.014 45.19 27.985 18838 18639 385 80 3540 8490 19 30 216 227 5.585
16 9668 9800 0 5142 137 132 40 10338 16132 15923 14266 14475 0 8073 217 209 81 360 27453 27814 24597 24957 .98 110 0 1.409 1.347 1.573 1.53 100 100 100 100 .649 .377 1.54 1.476 1.249 2.656 2.544 1.538 26261 23934 381 80 3700 8500 20 31 232 243 1.409
17 2658 2786 0 925 129 128 29 2353 33854 33659 38063 38258 0 11017 205 195 81 336 58033 58369 65626 65962 .99 120 0 4.624 4.626 15.041 14.247 100 98 100 100 .07 .041 14.305 14.32 1.316 24.663 24.69 13.961 36012 40721 425 120 3840 8490 19 31 246 258 4.624
18 23 149 0 277 126 126 27 138 318 127 71 262 0 201 201 191 75 329 219 548 122 452 .75 100 -50 2.412 1.337 1.155 46 36 48 26 1.087 .63 .92 3.087 3.475 1.587 5.322 .783 265 94 316 80 3980 8480 19 29 261 271 .666
19 4962 5090 0 1836 131 128 40 4481 1255 1063 1118 1310 0 469 210 192 201 331 1833 2164 1928 2259 .95 100 0 -1.29 -1.364 .242 .233 100 100 97 90 4.215 2.445 .237 .225 1.443 .409 .388 .23 5544 6080 313 80 4130 8490 20 30 276 286 -1.29
20 2735 2863 0 718 132 128 40 2599 1304 1119 1160 1345 0 341 206 185 188 319 1929 2248 2000 2319 .96 110 0 -.43 -.452 .432 .442 100 100 100 98 2.323 1.347 .431 .424 1.29 .742 .731 .414 3718 3895 364 80 4270 8490 19 30 289 300 -.43

Total number of rows: 43008

Table truncated, full table size 9413 Kbytes.




Supplementary data files not provided
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