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Sample GSM6230 Query DataSets for GSM6230
Status Public on Apr 15, 2004
Title AML 3
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 3
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=640650LaserPower=4.384.27
Lot batch = shco021
 
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 GPL317
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
1 111 302 0 156 200 191 59 123 505 400 389 494 0 228 108 105 27 114 435 549 423 537 .78 80 0 1.822 1.93 3.582 3.251 57 46 98 98 .308 .283 3.252 3.505 2.3 3.535 3.809 2.413 523 500 270 52 1730 7830 83 91 61 69 1.822
2 243 445 0 206 214 202 69 201 151 38 43 156 0 65 113 113 26 123 41 164 47 170 .51 60 0 -2.283 -2.378 .237 .279 71 62 59 37 5.289 4.866 .189 .177 2.354 .205 .192 .149 239 286 147 32 1880 7830 84 90 77 83 -2.283
3 1723 1926 0 670 745 203 4251 1531 238 126 142 254 0 84 214 112 755 122 137 259 154 276 .82 110 0 -3.483 -3.481 .085 .085 0 0 0 0 12.151 11.179 .082 .082 1.609 .089 .09 .08 1657 1865 412 80 2000 7820 80 91 86 97 -3.483
4 2277 2486 0 1905 227 209 71 2781 2761 2648 2406 2519 0 1717 121 113 36 123 2878 3001 2615 2738 .97 80 0 .05 .2 .995 .96 96 94 100 100 1.05 .966 .952 1.057 1.504 1.035 1.149 .921 5429 4683 268 52 2160 7840 84 92 104 112 .05
5 281 480 0 392 212 199 59 367 328 211 170 287 0 209 119 117 30 127 229 357 185 312 .91 80 0 -.678 -.605 .585 .547 75 61 80 71 1.739 1.6 .575 .605 1.771 .625 .658 .526 578 451 250 52 2310 7830 83 91 119 127 -.678
6 113 312 0 122 204 199 45 79 181 65 73 189 0 81 115 116 30 126 71 197 79 205 .69 60 0 -.161 -.51 .675 .6 62 56 68 56 1.215 1.118 .823 .646 2.367 .894 .702 .564 144 186 140 32 2460 7830 84 90 135 141 -.161
7 487 694 0 311 210 207 47 498 210 98 108 220 0 86 115 112 32 122 107 228 117 239 .82 80 0 -2.225 -2.053 .211 .209 86 86 73 65 5.082 4.675 .197 .222 1.892 .214 .241 .205 596 595 233 52 2600 7830 83 91 148 156 -2.225
8 1888 2085 0 1209 202 197 46 2035 2488 2372 2301 2417 0 1270 128 116 69 126 2578 2704 2501 2627 .97 90 0 .341 .406 1.236 1.182 96 96 100 100 .858 .789 1.166 1.219 1.409 1.267 1.325 1.12 4407 4189 256 52 2750 7830 82 91 162 171 .341
9 368 566 0 329 200 198 42 416 3813 3697 3541 3657 0 1983 131 116 74 126 4018 4145 3849 3975 .89 90 0 3.272 3.387 10.012 9.708 84 82 100 100 .113 .104 8.887 9.622 1.953 9.66 10.459 8.422 4113 3909 265 52 2890 7830 82 91 176 185 3.272
10 14 207 0 139 202 193 73 51 142 27 9 124 0 75 119 115 31 125 29 154 10 135 .63 100 -50 -.517 .546 .59 30 17 30 23 1.889 1.738 .529 .643 2.96 .575 .699 .381 78 23 325 80 3050 7810 80 90 192 202 -.797
11 1031 1218 0 659 192 187 53 1055 732 622 567 677 0 409 112 110 30 120 676 796 616 736 .95 120 0 -.642 -.742 .571 .555 95 95 95 95 1.696 1.56 .59 .55 1.587 .641 .598 .592 1677 1598 460 120 3170 7820 80 92 203 215 -.642
12 470 657 0 424 188 187 40 499 444 329 292 407 0 224 114 115 30 125 358 483 317 442 .9 80 0 -.481 -.566 .659 .676 86 82 92 86 1.517 1.395 .659 .621 2.177 .717 .675 .569 828 762 258 52 3340 7830 83 91 222 230 -.481
13 341 516 0 347 182 175 45 379 497 385 369 481 0 241 112 112 28 122 418 540 401 523 .91 90 0 .143 .234 1.05 .925 78 71 96 94 .984 .906 1.016 1.082 1.895 1.104 1.176 .839 764 710 247 52 3490 7830 82 91 236 245 .143
14 17 202 0 97 186 185 43 36 131 15 3 119 0 51 118 116 36 126 16 142 3 129 .45 100 -50 -2.382 .526 .548 35 26 26 12 2.4 2.208 .417 .176 3.148 .453 .192 .32 51 20 348 80 3630 7810 80 90 250 260 -1.143
15 1597 1791 0 1649 195 194 46 1853 1014 897 782 899 0 759 121 117 37 127 975 1102 850 977 .96 90 0 -.926 -.91 .551 .486 80 78 90 84 2.066 1.901 .484 .49 1.849 .526 .532 .462 2750 2379 258 52 3760 7820 81 90 263 272 -.926
16 770 964 0 426 199 194 52 725 792 678 641 755 0 344 118 114 37 124 737 861 697 821 .93 90 0 .024 -.144 1.073 .911 86 86 96 96 1.069 .984 .935 .832 1.966 1.016 .905 .882 1403 1411 324 52 3920 7820 81 90 279 288 .024
17 183 363 0 171 195 180 67 221 188 62 46 172 0 59 140 126 60 137 67 204 50 187 .57 50 0 -1.713 -1.872 .261 .273 91 66 41 25 3.565 3.279 .281 .251 2.024 .305 .273 .127 283 229 104 12 4090 7810 82 87 298 303 -1.713
18 56 241 0 109 187 185 35 62 2802 2676 2772 2898 0 1556 147 126 90 137 2909 3046 3013 3150 .71 90 0 5.552 5.75 29.677 27.65 55 44 100 98 .023 .021 43.161 49.5 1.642 46.914 53.804 27.659 2738 2828 232 52 4220 7830 82 91 309 318 5.552
19 707 894 0 316 191 187 43 669 845 727 750 868 0 301 127 118 62 128 790 918 815 943 .93 120 0 .24 .205 1.113 1.058 97 95 100 99 .92 .847 1.087 1.061 1.544 1.181 1.153 1.052 1396 1457 438 120 4350 7820 80 92 321 333 .24
20 412 602 0 329 206 190 76 424 397 281 219 335 0 230 122 116 34 126 305 432 238 364 .91 80 0 -.473 -.791 .566 .613 80 78 90 84 1.509 1.388 .663 .532 2.007 .72 .578 .649 705 631 239 52 4510 7810 81 89 339 347 -.473

Total number of rows: 43008

Table truncated, full table size 9008 Kbytes.




Supplementary data files not provided
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