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Sample GSM6307 Query DataSets for GSM6307
Status Public on Apr 15, 2004
Title AML 91
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 91
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=720650LaserPower=3.874.2
Lot batch = shdj074
 
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
1 439 559 0 161 124 120 37 401 1220 1115 1054 1159 0 444 134 105 129 128 1360 1488 1285 1413 .91 70 0 1.762 1.55 2.812 2.935 100 100 100 100 .36 .295 2.781 2.401 1.51 3.391 2.928 2.935 1516 1493 225 32 1550 8490 25 32 23 30 1.762
2 4073 4194 0 2075 125 121 38 4283 7099 6994 7011 7116 0 2936 123 105 112 128 8529 8657 8550 8678 .98 80 0 .994 1.07 1.778 1.632 100 100 100 100 .612 .502 1.633 1.721 1.474 1.991 2.099 1.59 11277 11084 292 52 1710 8500 26 34 39 47 .994
3 1071 1194 0 1250 124 123 30 1396 1170 1065 859 964 0 818 114 105 43 128 1299 1427 1048 1176 .96 60 0 -.104 -.032 .931 .771 96 90 100 96 1.311 1.075 .763 .802 1.763 .93 .978 .694 2461 1930 171 32 1860 8500 27 33 55 61 -.104
4 387 504 0 452 119 117 29 520 3762 3661 2949 3050 0 2807 110 101 47 123 4465 4588 3596 3720 .95 80 0 3.102 3.216 8.108 7.573 90 84 100 100 .142 .116 7.04 7.62 1.593 8.586 9.293 6.791 4181 3336 244 52 2010 8500 26 34 69 77 3.102
5 1233 1353 0 788 134 120 72 1282 2528 2421 2193 2300 0 1374 131 107 128 130 2952 3083 2674 2805 .96 70 0 1.204 1.117 1.922 1.802 100 100 100 100 .53 .434 1.888 1.779 1.47 2.303 2.169 1.839 3703 3426 211 32 2140 8490 25 32 82 89 1.204
6 876 995 0 344 125 119 30 814 517 413 429 533 0 187 109 104 38 127 504 630 523 650 .92 60 0 -.693 -.744 .498 .512 100 100 100 93 1.971 1.616 .507 .49 1.413 .619 .597 .488 1227 1305 164 32 2290 8500 27 33 98 104 -.693
7 1269 1395 0 937 131 126 34 1235 1836 1732 1685 1789 0 1253 108 104 39 127 2112 2239 2055 2182 .96 80 0 .774 .695 1.597 1.498 96 92 100 100 .713 .585 1.402 1.328 1.791 1.71 1.619 1.396 2967 2954 266 52 2430 8500 26 34 111 119 .774
8 624 746 0 408 125 122 32 602 353 253 238 338 0 173 107 100 46 122 309 430 290 412 .81 80 0 -.964 -1.104 .446 .427 94 92 92 80 2.379 1.951 .42 .381 2.249 .513 .465 .368 855 862 264 52 2580 8500 26 34 126 134 -.964
9 582 700 0 200 123 118 35 561 362 260 254 356 0 135 111 102 46 124 317 441 310 434 .85 90 0 -.823 -.91 .432 .445 100 100 96 88 2.158 1.769 .463 .436 1.63 .565 .532 .451 821 836 325 52 2730 8500 25 34 140 149 -.823
10 379 496 0 144 120 117 34 375 295 196 181 280 0 116 107 99 45 121 239 360 221 341 .73 60 0 -.65 -.78 .46 .5 100 96 93 81 1.913 1.569 .523 .478 2.281 .637 .582 .5 571 560 165 32 2880 8490 26 32 157 163 -.65
11 6978 7098 0 2089 124 120 34 7049 1034 930 930 1034 0 343 110 104 46 127 1134 1261 1134 1261 .95 90 0 -2.636 -2.621 .129 .131 100 100 100 100 7.58 6.215 .132 .133 1.321 .161 .163 .126 7979 7908 316 52 3020 8500 25 34 169 178 -2.636
12 11749 11878 0 5856 131 129 32 10734 15190 15083 17189 17296 0 7247 118 107 53 130 18394 18524 20962 21093 .99 90 0 .777 .835 1.521 1.391 100 100 100 100 .712 .584 1.405 1.463 1.333 1.714 1.784 1.38 25817 28938 312 52 3170 8490 24 33 184 193 .777
13 1547 1673 0 713 129 126 30 1444 3413 3305 3241 3349 0 1568 118 108 50 132 4030 4162 3952 4084 .95 90 0 1.481 1.353 2.402 2.351 100 100 100 100 .437 .358 2.289 2.095 1.498 2.791 2.555 2.297 4749 4788 301 52 3310 8490 24 33 198 207 1.481
14 434 560 0 160 131 126 34 436 486 378 371 479 0 127 116 108 46 132 461 593 452 584 .85 100 0 .08 .06 .867 .864 100 100 98 98 1.153 .946 .867 .855 1.593 1.057 1.042 .848 814 805 374 80 3460 8500 25 35 213 223 .08
15 568 694 0 200 131 126 33 549 10852 10737 10675 10790 0 3117 134 115 115 140 13094 13234 13018 13159 .96 90 0 4.576 4.519 20.473 19.775 100 98 100 100 .051 .042 19.557 18.794 1.337 23.85 22.92 20.097 11286 11243 270 52 3600 8490 24 33 227 236 4.576
16 3959 4083 0 3367 126 124 30 4556 11949 11840 10213 10322 0 7819 124 109 94 133 14439 14572 12455 12588 .97 120 0 1.664 1.654 3.054 2.619 100 98 100 100 .385 .316 2.599 2.58 1.748 3.169 3.146 2.524 16396 14172 458 120 3750 8500 24 36 241 253 1.664
17 2238 2359 0 930 124 121 30 1985 24791 24682 28306 28415 0 9743 112 109 44 133 30100 30233 34520 34652 .97 120 0 3.923 3.947 14.002 12.676 99 98 100 100 .08 .066 12.434 12.648 1.546 15.164 15.424 12.336 26667 30544 402 120 3900 8500 24 36 256 268 3.923
18 19 134 0 263 126 115 100 109 185 80 13 118 0 206 114 105 91 128 98 226 16 144 .7 100 -50 -.261 .733 .782 18 12 17 11 1.363 1.117 .734 .684 3.167 .895 .834 .6 189 32 315 80 4040 8490 24 34 271 281 -.16
19 5512 5625 0 2592 124 113 103 4741 1959 1860 1778 1877 0 956 114 99 94 121 2268 2389 2168 2289 .97 100 0 -1.064 -1.346 .413 .392 100 100 100 98 2.549 2.09 .392 .323 1.419 .478 .393 .374 6601 7290 295 80 4190 8500 25 35 286 296 -1.064
20 2731 2847 0 1250 120 116 37 2537 2160 2061 2260 2359 0 1026 107 99 46 121 2513 2634 2756 2877 .96 120 0 -.013 .013 .87 .839 98 97 100 100 1.231 1.009 .812 .828 1.534 .991 1.009 .806 4598 4991 417 120 4330 8500 24 36 299 311 -.013

Total number of rows: 43008

Table truncated, full table size 9349 Kbytes.




Supplementary data files not provided
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