NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6309 Query DataSets for GSM6309
Status Public on Apr 15, 2004
Title AML 32
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 32
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=3.863.16
Lot batch = shdj076
 
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
1 252 397 0 206 149 145 35 282 1101 979 1076 1198 0 523 127 122 41 126 1009 1135 1109 1235 .86 80 0 1.84 2.138 3.585 3.446 86 80 100 100 .288 .279 3.472 4.27 1.631 3.579 4.402 3.435 1261 1328 278 52 1560 8470 27 35 24 32 1.84
2 2774 2924 0 1361 152 150 39 2959 6539 6424 6371 6486 0 2713 125 115 54 119 6623 6741 6568 6687 .97 80 0 1.162 1.243 2.3 2.2 100 100 100 100 .461 .447 2.171 2.297 1.373 2.238 2.368 2.161 9383 9145 275 52 1710 8460 26 34 39 47 1.162
3 478 623 0 1011 149 145 34 946 1063 945 564 682 0 901 122 118 39 122 974 1096 581 703 .93 60 0 .042 .283 1.045 1.075 90 90 96 96 1.001 .971 .999 1.18 1.838 1.03 1.216 .92 1891 1042 172 32 1860 8470 28 34 55 61 .042
4 828 976 0 452 152 148 34 762 725 602 685 808 0 322 124 123 37 127 621 747 706 833 .89 70 0 -.296 -.23 .782 .729 100 96 96 96 1.266 1.228 .79 .827 2.595 .814 .853 .761 1364 1513 206 32 2000 8460 26 33 68 75 -.296
5 912 1062 0 492 153 150 34 907 1352 1224 1189 1317 0 531 131 128 45 132 1262 1394 1226 1358 .93 80 0 .476 .427 1.467 1.391 98 98 100 100 .741 .719 1.35 1.304 1.593 1.391 1.344 1.29 2131 2101 285 52 2150 8460 26 34 83 91 .476
6 657 805 0 339 152 148 34 632 665 541 576 700 0 286 127 124 43 128 558 686 594 722 .93 70 0 -.18 -.146 .828 .816 100 100 96 96 1.168 1.133 .856 .877 1.586 .882 .904 .798 1173 1233 215 32 2300 8470 27 34 98 105 -.18
7 1427 1575 0 828 152 148 33 1204 2788 2661 2991 3118 0 1366 132 127 51 131 2743 2874 3084 3214 .94 70 0 1.188 1.112 2.679 2.24 90 87 100 100 .452 .439 2.21 2.096 1.882 2.278 2.161 1.997 3865 4418 227 32 2440 8460 26 33 112 119 1.188
8 451 599 0 295 157 148 46 469 382 258 271 395 0 152 131 124 46 128 266 394 279 407 .87 70 0 -.818 -.691 .651 .614 93 84 90 84 1.818 1.763 .55 .601 2.13 .567 .619 .501 727 722 212 32 2590 8470 27 34 127 134 -.818
9 296 444 0 173 153 148 42 309 603 482 478 599 0 226 126 121 46 125 497 622 493 618 .87 100 0 .685 .735 1.715 1.543 95 91 98 97 .641 .622 1.56 1.615 1.835 1.608 1.665 1.567 791 774 403 80 2730 8470 26 36 140 150 .685
10 261 410 0 142 151 149 33 271 246 125 123 244 0 67 128 121 64 125 129 254 127 252 .69 60 0 -1.072 -1.041 .448 .443 93 90 84 50 2.168 2.103 .461 .471 1.961 .476 .486 .388 396 384 165 32 2880 8460 27 33 157 163 -1.072
11 3580 3724 0 1402 147 144 33 3158 607 487 473 593 0 234 124 120 39 124 502 626 488 611 .9 90 0 -2.653 -2.876 .161 .155 100 100 98 96 6.485 6.29 .154 .132 1.662 .159 .136 .134 3645 4053 340 52 3020 8460 25 34 169 178 -2.653
12 5875 6025 0 2921 155 150 40 5561 7911 7791 7990 8110 0 3513 133 120 73 124 8032 8156 8237 8361 .96 90 0 .53 .488 1.518 1.392 100 100 100 100 .714 .692 1.401 1.36 1.413 1.444 1.402 1.35 13352 13865 312 52 3170 8460 25 34 184 193 .53
13 966 1115 0 400 155 149 42 913 2138 2010 1750 1878 0 910 137 128 64 132 2072 2204 1804 1936 .92 90 0 1.182 .901 2.218 2.199 100 100 100 100 .454 .441 2.202 1.812 1.492 2.27 1.868 2.285 2923 2716 301 52 3310 8460 25 34 198 207 1.182
14 252 407 0 139 156 155 38 243 481 349 348 480 0 187 137 132 48 136 360 496 359 495 .81 100 0 .566 .51 1.456 1.398 95 85 97 87 .696 .675 1.436 1.381 1.867 1.481 1.424 1.508 592 600 368 80 3460 8470 26 36 213 223 .566
15 420 572 0 188 155 152 39 411 8468 8336 8796 8928 0 2678 211 132 549 136 8594 8730 9068 9204 .92 90 0 4.386 4.432 20.771 19.011 96 94 100 100 .049 .048 20.282 20.943 1.473 20.91 21.591 21.045 8747 9216 300 52 3600 8460 25 34 227 236 4.386
16 3945 4095 0 1872 152 150 39 3883 8073 7945 7586 7714 0 2723 189 128 488 132 8191 8323 7821 7953 .95 100 0 1.077 .987 2.249 2.001 100 100 100 100 .489 .474 2.046 1.923 1.471 2.109 1.982 1.932 11828 11531 382 80 3760 8470 26 36 243 253 1.077
17 1585 1729 0 564 148 144 32 1474 9349 9228 9854 9975 0 2561 126 121 51 125 9513 9638 10159 10284 .95 110 0 2.69 2.68 6.721 6.334 100 100 100 100 .16 .155 6.261 6.217 1.449 6.454 6.409 6.187 10702 11439 364 80 3900 8470 25 36 256 267 2.69
18 6 145 0 200 144 139 33 56 166 46 11 131 0 146 125 120 44 124 47 171 11 135 .78 100 -50 .918 .956 .927 26 18 26 13 1.217 1.181 .821 1.833 4.901 .847 1.89 .739 102 17 348 80 4050 8460 25 35 272 282 -.24
19 2832 2975 0 1127 151 143 81 2765 2379 2257 2330 2452 0 761 130 122 63 126 2327 2453 2402 2528 .95 90 0 -.249 -.238 .876 .816 100 100 100 100 1.225 1.188 .816 .823 1.577 .842 .848 .767 5022 5162 265 52 4190 8460 25 34 286 295 -.249
20 1409 1552 0 526 149 143 70 1386 1812 1696 1623 1739 0 627 122 116 55 120 1748 1868 1673 1793 .95 110 0 .335 .248 1.248 1.216 100 100 100 100 .817 .793 1.224 1.152 1.395 1.262 1.188 1.225 3082 3032 379 80 4340 8470 25 36 300 311 .335

Total number of rows: 43008

Table truncated, full table size 9368 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap