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Sample GSM6293 Query DataSets for GSM6293
Status Public on Apr 15, 2004
Title AML 44
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 44
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=4.014.1
Lot batch = shcz090
 
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
1 319 448 0 257 133 129 36 286 273 180 160 253 0 121 100 93 40 126 243 369 216 342 .76 90 0 -.234 -.561 .551 .535 76 67 82 73 1.589 1.176 .629 .502 2.408 .851 .678 .484 466 479 361 52 1770 7650 32 41 20 29 -.234
2 604 732 0 2348 129 128 28 2175 247 152 79 174 0 170 101 95 35 128 205 334 107 235 .86 100 0 -3.404 -2.5 .106 .079 92 83 63 50 14.309 10.589 .07 .131 3.069 .094 .177 .063 2327 683 366 80 1920 7650 32 42 35 45 -3.404
3 1072 1202 0 1233 132 130 30 1456 1140 1044 904 1000 0 806 102 96 34 130 1411 1541 1222 1351 .98 90 0 -.045 .188 .803 .743 90 86 100 94 1.395 1.032 .717 .843 1.525 .969 1.14 .68 2500 1976 320 52 2060 7650 32 41 49 58 -.045
4 732 871 0 348 145 139 44 669 256 161 157 252 0 85 101 95 35 128 218 346 212 341 .74 70 0 -1.621 -1.787 .257 .238 90 90 93 78 4.155 3.075 .241 .214 2.316 .325 .29 .193 830 889 220 32 2200 7650 33 40 64 71 -1.621
5 719 872 0 401 165 153 74 595 539 423 414 530 0 338 121 116 49 157 572 728 559 716 .9 60 0 -.058 -.362 .574 .603 87 81 87 71 1.407 1.041 .711 .576 2.023 .961 .778 .687 1018 1133 172 32 2340 7650 34 40 79 85 -.058
6 497 634 0 397 147 137 45 566 372 260 225 337 0 212 114 112 35 151 351 503 304 455 .85 60 0 -.688 -.709 .382 .453 93 87 84 75 2.177 1.611 .459 .453 2.273 .621 .612 .443 826 722 176 32 2490 7650 34 40 94 100 -.688
7 277 408 0 566 135 131 33 547 1783 1681 978 1080 0 1582 108 102 40 138 2272 2409 1322 1459 .96 90 0 2.054 2.254 3.443 3.014 78 76 100 96 .325 .241 3.073 3.531 2.197 4.153 4.771 2.999 2228 1255 325 52 2640 7660 33 42 107 116 2.054
8 348 478 0 286 132 130 31 369 179 82 65 162 0 79 103 97 36 131 111 242 88 219 .66 90 0 -1.736 -1.986 .235 .202 80 80 63 46 4.5 3.33 .222 .187 2.471 .3 .252 .201 451 413 308 52 2790 7670 34 43 122 131 -1.736
9 425 556 0 222 134 131 31 388 537 434 514 617 0 247 106 103 37 139 586 726 695 834 .95 60 0 .596 .709 1.037 1.11 90 90 93 90 .894 .662 1.119 1.209 1.364 1.512 1.634 1.088 822 939 165 32 2920 7650 34 40 137 143 .596
10 582 719 0 282 145 137 44 496 195 92 88 191 0 72 107 103 35 139 124 264 119 258 .72 90 0 -1.996 -2.291 .169 .205 90 88 73 61 5.391 3.99 .185 .151 2.485 .251 .204 .173 588 670 339 52 3070 7640 31 40 150 159 -1.996
11 524 655 0 1219 139 131 41 1102 406 304 148 250 0 324 104 102 34 138 411 549 200 338 .95 90 0 -1.424 -1.39 .354 .296 73 65 80 69 3.625 2.683 .276 .282 2.503 .373 .382 .262 1406 672 341 52 3220 7650 32 41 165 174 -1.424
12 2846 2988 0 1426 148 142 44 2603 2577 2472 2696 2801 0 1405 112 105 51 142 3341 3482 3643 3785 .97 70 0 .36 .356 1.004 .979 100 96 100 100 1.053 .779 .95 .947 1.609 1.283 1.28 .957 5075 5542 208 32 3370 7640 32 39 181 188 .36
13 831 972 0 1583 146 141 41 1281 1345 1243 962 1064 0 993 106 102 41 138 1680 1818 1300 1438 .9 80 -100 .646 1.187 1.264 96 94 98 98 1.031 .763 .97 1.158 1.715 1.311 1.564 .735 2524 1793 283 52 3510 7650 33 41 195 203 .391
14 379 513 0 93 133 134 32 365 310 200 206 316 0 75 110 110 36 149 270 419 278 427 .85 50 0 -.433 -.445 .523 .595 100 100 100 91 1.825 1.351 .548 .544 1.628 .74 .735 .558 565 585 98 12 3650 7640 33 38 210 215 -.433
15 323 456 0 298 133 133 27 325 7029 6926 6164 6267 0 5620 110 103 43 139 9359 9499 8330 8469 .97 100 0 4.848 4.689 21.388 20.384 73 70 98 97 .047 .035 21.311 19.084 1.462 28.798 25.789 20.581 7251 6487 414 80 3800 7650 32 42 223 233 4.848
16 2985 3116 0 3072 132 131 28 3484 6636 6533 5065 5168 0 5526 111 103 46 139 8828 8968 6845 6984 .99 100 0 1.341 1.197 2.163 1.946 95 93 100 100 .533 .395 1.875 1.697 1.723 2.534 2.293 1.85 10017 8050 362 80 3950 7650 32 42 238 248 1.341
17 514 643 0 638 130 129 28 659 3320 3213 2819 2926 0 2713 112 107 37 145 4342 4486 3809 3954 .96 110 0 2.72 2.89 5.816 4.967 78 73 98 97 .205 .152 4.876 5.484 1.886 6.589 7.411 4.693 3872 3333 407 80 4100 7660 32 43 252 263 2.72
18 433 561 0 169 129 128 32 389 207 90 90 207 0 68 126 117 46 158 122 280 122 280 .45 50 0 -1.677 -1.832 .227 .263 100 91 66 50 4.322 3.198 .231 .208 2.09 .313 .281 .17 479 523 90 12 4240 7630 32 37 269 274 -1.677
19 1509 1641 0 827 133 132 31 1428 807 701 790 896 0 375 109 106 37 143 947 1091 1068 1211 .96 70 0 -.592 -.499 .512 .49 100 100 96 93 2.037 1.507 .491 .524 1.394 .663 .707 .467 2129 2299 224 32 4380 7640 32 39 282 289 -.592
20 1266 1397 0 692 135 131 32 1077 1360 1250 1457 1567 0 708 115 110 35 149 1689 1838 1969 2118 .96 60 0 .649 .637 1.277 1.153 93 90 100 96 .862 .638 1.161 1.151 2.097 1.568 1.555 1.1 2327 2723 164 32 4530 7640 33 39 298 304 .649

Total number of rows: 43008

Table truncated, full table size 9361 Kbytes.




Supplementary data files not provided
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