NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6342 Query DataSets for GSM6342
Status Public on Apr 15, 2004
Title AML 8
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 8
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=770630LaserPower=4.493.89
Lot batch = shdj109
 
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
1 394 505 0 145 112 111 24 435 412 256 216 372 0 183 173 156 69 252 413 665 348 600 .71 60 0 -.075 -.178 .461 .622 100 100 87 68 1.699 1.054 .589 .548 2.283 .949 .884 .666 691 610 165 32 1510 8700 27 33 20 26 -.075
2 2822 2933 0 1076 112 111 26 2781 1466 1300 1342 1508 0 640 174 166 71 268 2097 2365 2165 2432 .94 80 0 -.407 -.383 .435 .466 100 100 100 98 2.139 1.326 .467 .476 1.411 .754 .767 .471 4081 4164 277 52 1650 8710 27 35 33 41 -.407
3 1023 1128 0 801 106 105 23 1220 407 245 237 399 0 157 169 162 70 261 395 656 382 644 .75 60 0 -1.626 -1.42 .217 .201 100 100 90 71 4.98 3.087 .201 .232 1.845 .324 .374 .17 1465 1260 170 32 1800 8710 28 34 49 55 -1.626
4 311 419 0 270 110 108 24 382 1109 940 734 903 0 644 175 169 67 273 1516 1789 1184 1456 .93 80 0 1.989 1.929 2.527 2.592 94 92 98 96 .406 .252 2.461 2.36 1.731 3.969 3.807 2.581 1322 1045 242 52 1950 8720 28 36 63 71 1.989
5 1116 1227 0 610 114 111 31 1115 1909 1739 1549 1719 0 1148 177 170 71 274 2805 3079 2498 2773 .95 80 0 1.331 1.163 1.491 1.6 100 100 100 100 .641 .398 1.56 1.388 1.455 2.516 2.239 1.696 2854 2665 272 52 2090 8700 26 34 77 85 1.331
6 792 900 0 256 114 108 35 783 801 631 572 742 0 423 182 170 73 274 1018 1292 923 1197 .85 60 0 .378 .22 .605 .75 100 100 90 87 1.241 .769 .806 .722 2.264 1.3 1.165 .969 1414 1364 160 32 2230 8710 28 34 92 98 .378
7 1300 1408 0 786 111 108 27 1419 1974 1799 1315 1490 0 1319 185 175 71 282 2902 3184 2121 2403 .94 70 0 1.032 .706 1.122 1.235 100 100 100 100 .789 .489 1.268 1.012 1.569 2.045 1.632 1.439 3218 2615 226 32 2390 8710 27 34 107 114 1.032
8 609 718 0 266 501 109 2374 600 364 191 151 324 0 149 271 173 598 279 308 587 244 523 .95 60 0 -.962 -1.322 .283 .252 0 0 3 0 3.141 1.948 .318 .248 2.208 .513 .4 .307 791 760 166 32 2520 8700 27 33 121 127 -.962
9 466 571 0 162 109 105 26 459 473 303 294 464 0 170 171 170 61 274 489 763 474 748 .77 80 0 .09 .025 .612 .568 100 100 96 88 1.515 .939 .66 .631 1.696 1.065 1.018 .722 762 760 287 52 2670 8700 26 34 135 143 .09
10 329 436 0 120 107 107 25 333 292 122 108 278 0 119 172 170 65 274 197 471 174 448 .49 60 0 -.759 -.917 .299 .356 100 100 59 43 2.73 1.692 .366 .328 3.086 .591 .529 .461 455 437 171 32 2820 8710 28 34 151 157 -.759
11 2231 2338 0 1058 108 107 23 2153 512 350 292 454 0 264 169 162 67 261 565 826 471 732 .81 100 0 -1.931 -2.244 .157 .164 100 100 88 72 6.151 3.814 .163 .131 1.952 .262 .211 .156 2503 2523 382 80 2970 8700 25 35 164 174 -1.931
12 4693 4798 0 3231 108 105 23 4914 3249 3081 2332 2500 0 2236 174 168 69 271 4969 5240 3761 4032 .96 110 0 .016 -.319 .616 .653 100 100 100 100 1.595 .989 .627 .497 1.595 1.011 .801 .642 7995 7025 368 80 3110 8710 25 36 177 188 .016
13 518 626 0 304 109 108 25 546 4090 3922 2859 3027 0 2960 171 168 67 271 6326 6597 4611 4882 .91 100 0 3.534 3.154 6.198 6.691 100 98 100 100 .139 .086 7.183 5.519 1.695 11.586 8.902 8.791 4468 3377 332 80 3260 8710 26 36 193 203 3.534
14 617 725 0 327 111 108 27 640 495 320 326 501 0 152 184 175 77 282 516 798 526 808 .7 110 0 -.31 -.231 .498 .517 100 100 97 85 2 1.24 .5 .528 1.895 .806 .852 .454 960 943 425 80 3400 8700 24 35 206 217 -.31
15 443 551 0 227 112 108 27 443 21226 21052 22649 22823 0 10250 187 174 79 281 33955 34235 36531 36811 .94 110 0 6.26 6.366 46.163 46.938 98 97 100 100 .021 .013 47.521 51.126 1.389 76.647 82.462 48.748 21495 23092 380 80 3560 8710 25 36 222 233 6.26
16 5541 5647 0 2170 108 106 23 5649 8199 8022 7585 7762 0 3008 184 177 75 285 12939 13224 12234 12519 .95 110 0 1.196 1.143 1.468 1.475 100 100 100 100 .704 .437 1.42 1.369 1.498 2.29 2.208 1.424 13671 13126 322 80 3700 8710 25 36 236 247 1.196
17 1289 1395 0 396 124 106 178 1195 9660 9491 10837 11006 0 3441 196 169 187 273 15308 15581 17479 17752 .95 120 0 3.679 3.761 7.734 7.748 98 97 100 100 .126 .078 7.942 8.407 1.494 12.81 13.56 8.481 10686 12126 378 120 3850 8710 25 37 251 263 3.679
18 11 113 0 106 105 102 26 44 232 68 49 213 0 123 176 164 71 265 110 374 79 344 .4 100 -50 2.845 2.892 2.455 35 22 41 18 .647 .401 1.545 4.455 3.937 2.493 7.185 2.435 112 60 303 80 3990 8700 25 35 266 276 1.318
19 2455 2557 0 701 107 102 37 2400 942 775 802 969 0 355 177 167 70 269 1250 1519 1294 1563 .92 110 0 -.941 -.924 .291 .324 100 100 96 93 3.097 1.92 .323 .327 1.696 .521 .527 .326 3175 3257 354 80 4140 8700 24 35 280 291 -.941
20 1205 1310 0 484 112 105 49 1188 804 640 647 811 0 345 171 164 68 265 1032 1297 1044 1308 .92 120 0 -.203 -.208 .501 .515 100 99 98 96 1.856 1.151 .539 .537 1.599 .869 .866 .559 1828 1852 438 120 4280 8710 25 37 294 306 -.203

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