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Sample GSM6288 Query DataSets for GSM6288
Status Public on Apr 15, 2004
Title AML 34
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 34
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=680650LaserPower=3.993.83
Lot batch = shcz085
 
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 GPL318
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
1 540 657 0 386 120 117 34 490 1410 1286 1438 1562 0 869 132 124 47 182 1891 2074 2115 2297 .92 90 0 1.948 1.969 2.26 2.541 82 80 94 92 .381 .259 2.624 2.663 2.461 3.86 3.916 2.595 1776 1978 357 52 1990 7640 47 56 26 35 1.948
2 4350 4469 0 3230 127 119 39 4379 8209 8081 7083 7211 0 5351 133 128 45 188 11884 12072 10416 10604 .96 90 0 1.44 1.26 2.191 1.89 100 100 100 100 .542 .368 1.845 1.628 1.794 2.714 2.395 1.805 12460 11433 300 52 2130 7640 47 56 40 49 1.44
3 2690 2812 0 2176 129 122 38 2930 2508 2377 2244 2375 0 1449 140 131 57 193 3496 3688 3300 3493 .96 90 0 .255 .295 .994 .818 100 98 100 100 1.233 .838 .811 .834 1.816 1.193 1.227 .746 5307 4934 331 52 2270 7640 47 56 54 63 .255
4 1175 1305 0 424 137 130 48 1153 1819 1681 1571 1709 0 632 151 138 68 203 2472 2675 2310 2513 .95 70 0 1.1 .975 1.484 1.433 100 100 100 100 .686 .466 1.458 1.337 1.465 2.144 1.966 1.469 2834 2746 218 32 2410 7640 48 55 69 76 1.1
5 953 1086 0 722 149 133 73 1031 1035 890 766 911 0 670 217 145 345 213 1309 1522 1126 1340 .85 80 0 .344 .241 .838 .788 96 94 73 55 1.158 .788 .863 .804 1.712 1.269 1.182 1.048 1921 1719 284 52 2560 7640 48 56 84 92 .344
6 1011 1133 0 499 132 122 50 979 1009 880 793 922 0 419 182 129 341 190 1294 1484 1166 1356 .94 70 0 .403 .206 .94 .96 100 100 90 68 1.113 .757 .899 .784 1.706 1.322 1.153 .88 1859 1804 226 32 2710 7640 48 55 99 106 .403
7 1823 1947 0 838 133 124 47 1771 2610 2487 2539 2662 0 967 133 123 57 181 3657 3838 3734 3915 .93 70 0 1.046 1.034 1.487 1.322 96 96 100 100 .712 .484 1.404 1.393 1.796 2.065 2.048 1.369 4258 4362 227 32 2850 7640 48 55 113 120 1.046
8 1066 1190 0 427 138 124 78 1002 366 237 249 378 0 117 134 129 44 190 349 538 366 556 .85 70 0 -1.524 -1.542 .235 .235 100 90 93 87 4.228 2.875 .237 .234 1.714 .348 .344 .223 1239 1315 232 32 3000 7640 48 55 128 135 -1.524
9 669 784 0 300 123 115 33 611 1007 880 888 1015 0 395 132 127 43 187 1294 1481 1306 1493 .88 60 0 1.083 .965 1.582 1.491 90 90 100 96 .694 .472 1.44 1.327 1.983 2.118 1.952 1.461 1491 1557 176 32 3150 7640 49 55 144 150 1.083
10 828 950 0 282 140 122 76 761 265 132 126 259 0 92 138 133 48 196 194 390 185 381 .74 70 0 -1.971 -2.16 .153 .15 93 93 81 62 5.765 3.92 .173 .152 1.75 .255 .224 .175 893 954 227 32 3290 7640 48 55 157 164 -1.971
11 2832 2953 0 2349 125 121 34 3193 881 756 682 807 0 479 131 125 41 184 1112 1296 1003 1187 .93 60 0 -1.522 -1.498 .282 .251 100 100 100 93 4.224 2.872 .237 .241 2.199 .348 .354 .21 3949 3514 172 32 3450 7640 49 55 174 180 -1.522
12 4141 4268 0 2918 141 127 79 4134 3573 3450 3338 3461 0 2213 138 123 59 181 5074 5254 4909 5090 .94 60 0 .295 .245 1.077 .869 96 90 100 100 1.198 .815 .835 .806 2.529 1.227 1.185 .779 7584 7479 172 32 3580 7640 49 55 187 193 .295
13 1036 1159 0 526 123 123 32 1081 1513 1383 1295 1425 0 681 132 130 37 191 2034 2225 1904 2096 .85 60 0 .912 .878 1.258 1.179 96 96 100 100 .782 .532 1.279 1.25 1.804 1.881 1.838 1.267 2464 2331 176 32 3730 7640 49 55 202 208 .912
14 283 400 0 196 124 117 32 297 401 270 228 359 0 147 134 131 35 193 397 590 335 528 .84 60 0 .419 .245 .792 .776 90 87 96 96 1.1 .748 .909 .806 2.395 1.337 1.185 .848 567 511 170 32 3880 7640 49 55 217 223 .419
15 575 693 0 380 122 118 31 560 14187 14057 13358 13488 0 8950 141 130 105 191 20672 20863 19644 19835 .93 90 0 5.206 5.094 22.563 23.313 92 90 100 100 .04 .027 25.102 23.231 1.514 36.914 34.164 26.333 14617 13933 342 52 4020 7640 47 56 229 238 5.206
16 7408 7526 0 3778 127 118 107 6034 14348 14221 16192 16319 0 7616 139 127 106 187 20913 21100 23812 23999 .95 90 0 1.793 1.685 2.659 2.291 96 96 100 100 .424 .289 2.357 2.186 1.714 3.466 3.214 2.294 20255 23600 337 52 4170 7640 47 56 244 253 1.793
17 867 982 0 902 118 115 32 1065 9502 9380 8668 8790 0 6646 127 122 42 179 13794 13974 12747 12926 .94 100 0 3.695 3.878 9.871 8.388 90 85 100 100 .114 .077 8.808 9.998 2.07 12.952 14.702 8.59 10445 9535 404 80 4330 7640 47 57 260 270 3.695
18 664 788 0 190 132 124 54 659 293 172 172 293 0 51 128 121 41 178 253 431 253 431 .78 50 0 -1.381 -1.392 .259 .246 100 100 100 91 3.831 2.605 .261 .259 1.395 .384 .381 .215 831 836 92 12 4450 7640 49 54 274 279 -1.381
19 2618 2740 0 1668 135 122 91 2703 1269 1138 1258 1389 0 676 136 131 50 193 1674 1866 1850 2043 .94 70 0 -.692 -.501 .474 .397 93 93 100 96 2.375 1.615 .421 .481 2.37 .619 .707 .395 3841 3876 228 32 4620 7640 48 55 290 297 -.692
20 2486 2608 0 1307 127 122 37 2288 1883 1755 1829 1957 0 921 132 128 45 188 2581 2769 2690 2878 .97 70 0 .174 .114 .794 .749 100 100 100 100 1.304 .887 .767 .736 1.626 1.128 1.082 .728 4043 4315 212 32 4760 7640 48 55 304 311 .174

Total number of rows: 43008

Table truncated, full table size 9456 Kbytes.




Supplementary data files not provided
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