NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6340 Query DataSets for GSM6340
Status Public on Apr 15, 2004
Title AML 73
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 73
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=4.53.73
Lot batch = shdj107
 
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
1 603 726 0 257 126 123 32 597 1740 1585 1551 1706 0 542 174 155 206 225 2297 2522 2248 2472 .88 70 0 1.944 1.898 2.789 2.406 100 100 100 100 .377 .26 2.655 2.572 1.677 3.848 3.728 2.792 2182 2154 212 32 1610 8790 19 26 13 20 1.944
2 4960 5084 0 2633 128 124 34 4948 3327 3172 3623 3778 0 1586 191 155 329 225 4597 4822 5251 5475 .96 90 0 -.106 .082 .731 .65 100 98 98 92 1.56 1.076 .641 .73 1.788 .929 1.059 .61 8120 8583 301 52 1750 8800 19 28 26 35 -.106
3 52 177 0 840 128 125 33 396 433 288 73 218 0 531 149 145 54 210 417 628 106 316 .94 100 -100 1.025 1.232 .818 55 46 55 40 1.375 .949 .727 1.404 3.519 1.054 2.035 .631 684 125 378 80 1910 8780 17 27 42 52 .076
4 496 620 0 514 128 124 32 580 1210 1063 1010 1157 0 795 158 147 58 213 1541 1754 1464 1677 .86 80 0 1.409 1.561 2.26 1.894 92 76 96 92 .546 .376 1.833 2.036 3.326 2.656 2.951 1.795 1643 1506 210 52 2050 8800 20 28 57 65 1.409
5 1418 1545 0 1221 130 127 32 1573 2843 2690 2385 2538 0 1782 157 153 57 222 3899 4120 3457 3678 .93 80 0 1.309 1.285 1.96 1.64 86 84 100 98 .585 .403 1.71 1.682 2.172 2.478 2.438 1.641 4263 3803 274 52 2190 8790 19 27 71 79 1.309
6 1405 1530 0 582 129 125 30 1223 1513 1361 1471 1623 0 497 161 152 58 220 1972 2193 2132 2352 .94 70 0 .69 .602 1.227 1.054 96 93 100 100 .899 .62 1.113 1.047 1.714 1.613 1.517 1.046 2584 2876 230 32 2340 8790 19 26 86 93 .69
7 1952 2080 0 1717 168 128 324 2135 3760 3597 3445 3608 0 1989 228 163 384 236 5213 5449 4993 5229 .93 70 0 1.288 1.355 2.512 2.008 78 75 96 90 .594 .41 1.685 1.765 2.457 2.442 2.558 1.46 5732 5397 207 32 2510 8800 20 27 103 110 1.288
8 1117 1246 0 531 134 129 50 1062 490 332 312 470 0 175 161 158 54 229 481 710 452 681 .82 70 0 -1.142 -1.305 .307 .27 96 96 100 93 3.199 2.207 .313 .279 1.784 .453 .405 .291 1394 1429 202 32 2630 8790 19 26 115 122 -1.142
9 738 860 0 346 128 122 45 693 1305 1152 1113 1266 0 418 164 153 68 222 1670 1891 1613 1835 .89 90 0 1.269 1.128 1.942 1.582 94 90 100 98 .602 .415 1.662 1.508 2.05 2.409 2.186 1.575 1845 1851 348 52 2770 8790 18 27 128 137 1.269
10 409 533 0 290 127 124 34 442 422 277 242 387 0 163 154 145 61 210 401 612 351 561 .8 70 0 -.139 -.222 .722 .701 96 93 93 78 1.596 1.101 .627 .592 2.215 .908 .858 .575 719 651 211 32 2930 8790 19 26 145 152 -.139
11 6917 7038 0 2926 129 121 62 6458 1196 1049 1111 1258 0 577 158 147 65 213 1520 1733 1610 1823 .89 80 0 -2.087 -2.103 .155 .178 100 100 100 92 6.156 4.248 .162 .161 1.581 .235 .233 .154 7507 8028 258 52 3060 8800 20 28 158 166 -2.087
12 7196 7316 0 7391 127 120 53 8349 6002 5856 5724 5870 0 3902 156 146 61 212 8487 8699 8296 8507 .92 100 0 .024 .205 1.291 .755 92 88 100 100 1.426 .984 .701 .795 4.145 1.017 1.153 .592 14205 12920 389 80 3220 8790 18 28 173 183 .024
13 1213 1334 0 679 126 121 34 1093 2768 2623 2609 2754 0 1516 150 145 50 210 3801 4012 3781 3991 .92 90 0 1.798 1.64 2.585 2.144 98 94 100 100 .417 .288 2.4 2.151 1.796 3.478 3.117 2.34 3716 3822 259 52 3360 8790 18 27 187 196 1.798
14 341 465 0 185 129 124 35 347 953 807 759 905 0 397 152 146 54 212 1170 1381 1100 1312 .89 120 0 1.753 1.69 2.433 2.215 95 91 98 98 .43 .297 2.326 2.226 1.901 3.371 3.226 2.452 1154 1100 480 120 3510 8790 17 29 201 213 1.753
15 415 540 0 262 130 125 32 399 9569 9414 9868 10023 0 3959 160 155 55 225 13643 13868 14301 14526 .88 100 0 5.096 5.107 23.003 22.19 86 80 100 100 .042 .029 23.594 23.778 1.588 34.194 34.461 23.351 9813 10283 338 80 3660 8790 18 28 217 227 5.096
16 7317 7441 0 3505 130 124 36 7342 13566 13411 12532 12687 0 4681 162 155 59 225 19436 19661 18162 18387 .94 110 0 1.405 1.312 2.023 1.724 98 98 100 100 .547 .378 1.827 1.713 1.967 2.647 2.482 1.739 20753 19849 403 80 3810 8790 17 28 231 242 1.405
17 1874 1996 0 771 125 122 34 1673 35966 35820 38715 38861 0 9891 155 146 61 212 51913 52125 56109 56320 .93 120 0 4.956 4.904 20.745 20.275 95 93 100 100 .047 .032 21.411 20.659 1.326 31.03 29.941 21.068 37493 40589 442 120 3960 8790 17 29 246 258 4.956
18 22 143 0 252 124 121 30 76 198 58 34 174 0 122 151 140 56 203 84 287 49 252 .62 100 -50 1.163 1.252 .917 40 18 38 21 1.31 .904 .763 1.545 4.582 1.106 2.24 .453 134 56 328 80 4100 8780 17 27 261 271 .145
19 4081 4203 0 1036 126 122 33 3991 1366 1226 1218 1358 0 320 148 140 50 203 1777 1980 1765 1968 .9 90 0 -1.167 -1.209 .31 .289 100 100 100 100 3.255 2.246 .307 .298 1.463 .445 .433 .279 5217 5299 252 52 4240 8790 18 27 275 284 -1.167
20 2028 2149 0 740 124 121 33 1873 968 819 826 975 0 328 155 149 60 216 1187 1403 1197 1413 .9 110 0 -.658 -.761 .463 .433 98 95 96 96 2.287 1.578 .437 .407 1.703 .634 .59 .407 2692 2854 394 80 4380 8790 17 28 288 299 -.658

Total number of rows: 43008

Table truncated, full table size 9383 Kbytes.




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