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Sample GSM6329 Query DataSets for GSM6329
Status Public on Apr 15, 2004
Title AML 89
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 89
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=710650LaserPower=4.394.32
Lot batch = shdj096
 
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
1 485 615 0 301 134 130 37 494 2189 2039 2175 2325 0 985 156 150 64 172 2344 2516 2500 2672 .9 80 0 2.246 2.366 4.223 4.23 92 90 100 98 .242 .211 4.128 4.485 1.81 4.744 5.155 4.209 2533 2660 268 52 1520 8300 26 34 16 24 2.246
2 2611 2744 0 2593 137 133 36 2977 1863 1713 1413 1563 0 1351 158 150 60 172 1969 2141 1624 1797 .94 100 0 -.596 -.685 .738 .558 93 93 96 88 1.738 1.512 .575 .541 3.051 .661 .622 .53 4690 4024 374 80 1670 8300 25 35 30 40 -.596
3 1669 1804 0 1453 137 135 28 1916 1890 1742 1804 1952 0 1084 149 148 55 170 2002 2172 2074 2244 .9 60 0 .064 .313 1.248 .864 90 90 100 100 1.1 .957 .909 1.081 2.903 1.045 1.242 .808 3658 3473 164 32 1810 8290 26 32 46 52 .064
4 748 884 0 617 146 136 113 719 729 573 513 669 0 338 159 156 61 179 659 838 590 769 .82 70 0 -.127 -.343 1.219 .851 78 59 96 93 1.255 1.092 .797 .686 3.488 .916 .788 .621 1292 1261 196 32 1970 8290 25 32 61 68 -.127
5 1388 1525 0 1035 139 137 33 1327 2530 2379 2128 2279 0 1729 155 151 53 174 2734 2908 2446 2620 .91 80 0 1.043 .817 1.944 1.762 88 86 96 96 .558 .485 1.793 1.533 1.936 2.061 1.762 1.789 3706 3516 278 52 2100 8290 25 33 74 82 1.043
6 1176 1310 0 553 140 134 54 1058 1974 1830 1776 1920 0 741 149 144 49 166 2103 2269 2041 2207 .91 70 0 .991 .796 2.043 1.723 96 96 100 100 .578 .503 1.73 1.51 2.102 1.988 1.736 1.706 2888 2952 225 32 2250 8290 25 32 89 96 .991
7 1916 2045 0 1240 134 129 34 1649 2931 2794 2846 2983 0 1818 142 137 45 157 3211 3369 3271 3429 .92 80 0 .962 .772 1.937 1.564 96 94 100 100 .59 .513 1.694 1.485 2.447 1.948 1.707 1.654 4443 4762 265 52 2400 8300 26 34 104 112 .962
8 692 823 0 388 137 131 37 627 786 641 663 808 0 382 151 145 48 167 737 903 762 929 .88 80 0 .233 .139 1.174 .91 96 90 100 96 .978 .851 1.022 .958 2.168 1.175 1.101 1.023 1268 1355 254 52 2540 8290 25 33 118 126 .233
9 609 743 0 293 137 134 34 630 1065 911 991 1145 0 325 157 154 55 177 1047 1224 1139 1316 .91 90 0 .733 .903 1.581 1.525 98 98 100 100 .692 .602 1.446 1.627 1.617 1.662 1.87 1.392 1541 1600 316 52 2690 8290 24 33 132 141 .733
10 483 622 0 151 140 139 31 466 507 358 344 493 0 192 152 149 54 171 411 583 395 567 .79 60 0 -.179 -.289 .672 .707 100 100 96 90 1.302 1.132 .768 .712 2.113 .883 .819 .778 824 827 165 32 2830 8290 26 32 148 154 -.179
11 6078 6216 0 2561 140 138 36 6051 1423 1281 1190 1332 0 646 150 142 54 163 1472 1636 1368 1531 .88 90 0 -2.039 -2.152 .206 .196 100 100 100 98 4.724 4.11 .212 .196 1.67 .243 .225 .183 7332 7268 328 52 2980 8290 24 33 161 170 -2.039
12 7793 7929 0 5116 139 136 32 8556 13726 13582 13573 13717 0 6898 153 144 56 166 15611 15777 15601 15767 .89 90 0 .868 1.001 1.764 1.459 100 100 100 100 .63 .548 1.587 1.742 1.887 1.825 2.002 1.553 22138 21366 300 52 3120 8290 24 33 175 184 .868
13 1118 1253 0 604 138 135 33 1072 3984 3831 3580 3733 0 2167 157 153 52 176 4403 4579 4115 4291 .9 100 0 2.038 1.88 3.617 3.756 93 91 100 100 .28 .243 3.574 3.202 2.073 4.108 3.681 3.918 4903 4698 342 80 3270 8290 24 34 190 200 2.038
14 398 534 0 177 138 136 33 410 1138 993 1037 1182 0 473 148 145 46 167 1141 1308 1192 1359 .9 120 0 1.477 1.582 2.449 2.432 96 95 99 97 .413 .359 2.422 2.606 1.89 2.784 2.995 2.69 1403 1435 442 120 3420 8290 23 35 204 216 1.477
15 842 979 0 539 139 137 34 846 24503 24354 24386 24535 0 12938 154 149 51 171 27993 28164 28030 28201 .92 100 0 5.048 5.057 26.84 27.206 92 90 100 100 .035 .03 28.787 28.962 1.585 33.089 33.29 29.087 25200 25228 315 80 3560 8290 24 34 219 229 5.048
16 5808 5939 0 3311 135 131 34 6442 16474 16325 15238 15387 0 7531 158 149 65 171 18764 18936 17515 17686 .92 110 0 1.542 1.592 2.732 2.383 100 100 100 100 .395 .343 2.534 2.624 1.789 2.913 3.016 2.593 22767 21046 378 80 3710 8290 23 34 233 244 1.542
17 2589 2720 0 976 134 131 31 2290 22915 22765 26149 26299 0 8786 162 150 79 172 26167 26339 30056 30229 .95 120 0 3.514 3.537 10.273 9.672 100 100 100 100 .101 .088 9.941 10.1 1.673 11.426 11.609 10.23 25055 28738 425 120 3860 8290 23 35 248 260 3.514
18 13 148 0 303 138 135 37 106 246 98 22 170 0 226 158 148 97 170 113 283 25 195 .65 100 -50 .96 1.652 1.723 31 17 30 13 1.082 .941 .925 1.692 4.285 1.063 1.945 .918 204 35 318 80 4000 8280 23 33 263 273 .088
19 4179 4314 0 1870 139 135 36 3635 2807 2665 2706 2848 0 1169 153 142 100 163 3063 3226 3110 3274 .92 100 0 -.247 -.426 .842 .721 96 95 100 100 1.364 1.187 .733 .648 2.578 .843 .744 .68 6300 6885 305 80 4150 8290 24 34 278 288 -.247
20 2021 2158 0 880 139 137 36 1852 2154 2009 2129 2274 0 815 151 145 53 167 2309 2476 2447 2614 .93 120 0 .318 .276 1.114 1.055 96 95 99 99 .922 .802 1.085 1.053 1.874 1.247 1.211 1.037 3861 4150 421 120 4300 8290 23 35 292 304 .318

Total number of rows: 43008

Table truncated, full table size 9510 Kbytes.




Supplementary data files not provided
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