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Sample GSM6308 Query DataSets for GSM6308
Status Public on Apr 15, 2004
Title AML 30
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 30
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=3.873.98
Lot batch = shdj075
 
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
1 289 433 0 201 146 144 32 326 662 532 484 614 0 287 137 130 46 137 560 697 509 646 .86 80 0 .781 .818 1.722 1.639 94 90 96 96 .613 .582 1.632 1.675 2.052 1.718 1.763 1.66 858 773 266 52 1630 8430 35 43 23 31 .781
2 4033 4179 0 1863 147 146 35 4077 1033 900 926 1059 0 445 137 133 43 140 947 1087 975 1115 .93 80 0 -2.106 -2.049 .214 .209 100 100 100 100 4.53 4.304 .221 .23 1.552 .232 .242 .208 4977 4959 277 52 1780 8420 34 42 38 46 -2.106
3 841 985 0 1027 143 144 37 1203 779 654 486 611 0 452 129 125 41 132 688 820 512 643 .94 60 0 -.805 -.717 .661 .578 100 100 96 93 1.839 1.747 .544 .578 1.73 .572 .608 .472 1857 1327 158 32 1930 8430 36 42 54 60 -.805
4 631 769 0 415 142 138 35 651 3332 3209 3181 3304 0 1809 131 123 43 129 3378 3507 3348 3478 .91 80 0 2.375 2.408 5.115 5.075 100 98 100 100 .203 .193 4.929 5.041 1.7 5.189 5.307 5.183 3860 3812 254 52 2070 8430 35 43 67 75 2.375
5 1150 1289 0 655 142 139 35 1087 1621 1494 1337 1464 0 867 132 127 45 134 1573 1706 1407 1541 .92 80 0 .533 .291 1.428 1.365 98 98 100 100 .728 .691 1.374 1.163 1.898 1.447 1.224 1.366 2581 2487 259 52 2220 8420 34 42 82 90 .533
6 669 818 0 334 149 149 35 678 972 836 846 982 0 445 138 136 46 143 880 1023 891 1034 .91 70 0 .376 .413 1.148 1.162 100 100 100 96 .811 .77 1.233 1.265 1.699 1.298 1.331 1.287 1514 1515 204 32 2360 8430 35 42 96 103 .376
7 1281 1432 0 850 154 151 37 1234 2183 2054 2132 2261 0 1033 132 129 43 136 2162 2298 2244 2380 .95 70 0 .809 .809 2.258 1.879 93 90 100 100 .601 .571 1.665 1.664 2.21 1.752 1.752 1.518 3288 3413 220 32 2510 8420 34 41 111 118 .809
8 947 1088 0 5782 147 141 46 4281 1362 1228 362 496 0 1512 135 134 41 141 1293 1434 381 522 .95 70 -100 -1.313 .248 .27 100 100 93 81 3.486 3.312 .287 .382 2.206 .302 .402 .255 5509 1309 202 32 2640 8430 35 42 124 131 -1.728
9 389 525 0 177 140 136 42 400 992 862 879 1009 0 383 136 130 46 137 907 1044 925 1062 .89 90 0 1.182 1.25 2.088 2.252 98 96 100 96 .464 .441 2.155 2.26 1.733 2.268 2.379 2.307 1262 1268 360 52 2790 8420 33 42 138 147 1.182
10 411 553 0 129 149 142 41 371 248 113 102 237 0 59 142 135 46 142 119 261 107 249 .76 50 0 -1.641 -1.937 .287 .349 100 91 83 58 3.283 3.119 .305 .248 1.768 .321 .261 .327 484 513 104 12 2940 8420 35 40 155 160 -1.641
11 2821 2951 0 1439 138 130 49 2966 576 442 387 521 0 283 139 134 45 141 465 606 407 548 .91 100 0 -2.672 -2.792 .135 .15 100 100 97 88 6.71 6.375 .149 .137 1.863 .157 .144 .148 3408 3208 415 80 3090 8430 34 44 168 178 -2.672
12 6089 6217 0 4231 132 128 33 6588 5600 5463 4489 4626 0 3575 145 137 51 144 5751 5895 4725 4869 .97 100 0 -.196 -.366 .833 .827 100 100 100 100 1.206 1.146 .829 .737 1.536 .873 .776 .829 12051 10578 369 80 3240 8430 34 44 183 193 -.196
13 1104 1233 0 474 135 129 49 1153 641 506 494 629 0 229 141 135 45 142 533 675 520 662 .92 90 0 -1.114 -1.086 .426 .412 100 100 100 98 2.279 2.165 .439 .447 1.409 .462 .471 .423 1659 1598 270 52 3380 8420 33 42 197 206 -1.114
14 304 437 0 170 137 133 46 321 399 268 251 382 0 152 137 131 44 138 282 420 264 402 .8 120 0 -.186 -.202 .86 .864 96 91 95 90 1.198 1.138 .835 .826 2.027 .879 .869 .815 589 555 500 120 3530 8430 33 45 211 223 -.186
15 822 951 0 404 133 129 32 764 1251 1124 1110 1237 0 467 131 127 40 134 1183 1317 1168 1302 .93 100 0 .631 .507 1.601 1.466 93 91 100 100 .68 .646 1.471 1.35 1.755 1.549 1.421 1.403 1888 1932 311 80 3680 8420 33 43 227 237 .631
16 3246 3375 0 2279 133 129 33 3430 8672 8542 8238 8368 0 5451 133 130 41 137 8992 9128 8672 8808 .94 120 0 1.39 1.418 2.697 2.542 97 94 100 100 .402 .381 2.49 2.538 2.147 2.621 2.671 2.563 11972 11484 425 120 3820 8430 33 45 240 252 1.39
17 1611 1744 0 737 136 133 38 1466 16698 16570 17486 17614 0 7679 133 128 41 135 17442 17577 18406 18541 .95 120 0 3.573 3.514 11.347 11.072 96 95 100 100 .088 .084 11.303 10.854 1.733 11.898 11.425 11.634 18036 19097 396 120 3970 8430 33 45 255 267 3.573
18 17 148 0 85 134 131 33 44 157 36 29 150 0 50 126 121 42 127 38 165 31 158 .08 100 -50 .845 1.385 1.364 36 20 37 11 1.222 1.161 .818 1.706 5.458 .861 1.796 .194 80 46 291 80 4110 8420 33 43 270 280 -.216
19 2843 2979 0 1372 137 136 34 2774 2584 2458 2469 2595 0 1266 132 126 46 133 2587 2720 2599 2732 .95 100 0 -.1 -.129 .879 .887 100 100 100 100 1.129 1.072 .886 .868 1.594 .933 .914 .885 5232 5312 301 80 4260 8420 33 43 285 295 -.1
20 1869 2006 0 614 138 137 31 1893 2290 2154 2015 2151 0 795 137 136 47 143 2267 2411 2121 2264 .95 110 0 .26 .183 1.112 1.17 100 100 100 100 .879 .835 1.138 1.078 1.333 1.198 1.135 1.172 4047 3884 326 80 4400 8430 33 44 298 309 .26

Total number of rows: 43008

Table truncated, full table size 9373 Kbytes.




Supplementary data files not provided
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