NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6299 Query DataSets for GSM6299
Status Public on Apr 15, 2004
Title AML 9
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 9
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=3.984.7
Lot batch = shdj066
 
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
1 272 395 0 145 279 123 1299 272 535 437 392 490 0 210 323 98 1702 156 694 849 622 778 .89 80 0 1.351 1.194 1.577 1.53 0 0 0 0 .622 .392 1.607 1.441 1.568 2.55 2.288 1.644 709 664 267 52 1530 8650 49 57 29 37 1.351
2 4948 5072 0 2361 127 124 36 4895 1677 1590 1471 1558 0 883 94 87 45 138 2524 2662 2335 2473 .94 80 0 -.956 -1.083 .314 .32 100 98 98 96 3.079 1.94 .325 .297 1.732 .516 .472 .323 6485 6419 296 52 1680 8640 48 56 44 52 -.956
3 1628 1754 0 893 133 126 68 1364 702 614 653 741 0 335 99 88 60 140 975 1114 1037 1176 .93 70 0 -.485 -.651 .552 .451 93 90 96 93 2.221 1.4 .45 .401 2.119 .715 .637 .396 1978 2281 215 32 1830 8650 49 56 59 66 -.485
4 864 994 0 420 128 130 32 795 291 205 188 274 0 126 93 86 39 137 325 462 298 435 .83 60 0 -1.289 -1.534 .266 .268 93 90 90 78 3.878 2.443 .258 .218 2.534 .409 .345 .229 1000 1052 135 32 1970 8650 50 56 74 80 -1.289
5 1222 1349 0 791 132 127 46 1305 1177 1083 1052 1146 0 633 100 94 47 149 1719 1868 1670 1819 .91 80 0 .398 .45 .907 .828 98 98 100 100 1.205 .759 .83 .861 1.972 1.317 1.366 .796 2388 2274 284 52 2110 8640 48 56 87 95 .398
6 942 1070 0 403 131 128 33 960 515 424 466 557 0 212 94 91 31 144 673 817 740 884 .89 60 0 -.512 -.349 .416 .462 100 100 100 100 2.264 1.426 .442 .495 1.628 .701 .785 .415 1384 1408 160 32 2270 8650 50 56 104 110 -.512
7 1344 1470 0 892 131 126 43 1540 1665 1574 1334 1425 0 871 108 91 109 144 2498 2643 2117 2262 .85 70 0 .698 .656 1.085 1.059 100 100 100 100 .978 .616 1.022 .993 1.743 1.622 1.575 1.011 3114 2678 210 32 2400 8650 49 56 116 123 .698
8 640 762 0 288 137 122 63 644 197 108 112 201 0 67 106 89 98 141 171 313 178 319 .74 70 0 -1.909 -1.848 .177 .174 100 96 56 12 5.963 3.757 .168 .175 1.703 .266 .278 .156 752 752 232 32 2540 8640 48 55 130 137 -1.909
9 433 561 0 218 137 128 61 454 1093 1002 1069 1160 0 385 100 91 63 144 1590 1735 1697 1841 .9 90 0 1.809 1.97 2.367 2.046 96 90 100 98 .453 .285 2.207 2.469 1.693 3.503 3.919 2.215 1456 1502 348 52 2700 8650 48 57 145 154 1.809
10 437 563 0 120 125 126 31 407 252 154 165 263 0 65 101 98 34 156 244 400 262 417 .78 50 0 -.736 -.739 .362 .348 100 100 100 91 2.643 1.665 .378 .378 1.708 .601 .599 .339 561 602 104 12 2840 8640 49 54 161 166 -.736
11 5515 5644 0 1735 131 129 34 5279 523 433 428 518 0 183 96 90 41 143 687 830 679 822 .92 90 0 -2.941 -3.021 .082 .082 100 100 100 100 12.192 7.681 .082 .078 1.624 .13 .123 .079 5712 5943 346 52 2990 8640 47 56 174 183 -2.941
12 8671 8799 0 4546 132 128 36 9212 4359 4265 4018 4112 0 2079 104 94 62 149 6770 6919 6378 6527 .97 90 0 -.444 -.443 .479 .473 100 100 100 100 2.16 1.361 .463 .463 1.477 .735 .736 .453 13477 12689 312 52 3140 8640 47 56 189 198 -.444
13 1197 1325 0 535 133 128 46 1210 1437 1340 1370 1467 0 660 111 97 71 154 2127 2281 2175 2329 .94 90 0 .814 .861 1.064 1.128 100 100 100 100 .903 .569 1.107 1.145 1.553 1.758 1.817 1.162 2550 2567 301 52 3280 8640 47 56 203 212 .814
14 322 452 0 135 136 130 58 341 499 413 411 497 0 162 95 86 47 137 656 792 652 789 .9 100 0 .943 1.019 1.211 1.196 100 98 100 100 .826 .52 1.211 1.276 1.477 1.922 2.026 1.231 754 733 368 80 3430 8650 48 58 218 228 .943
15 940 1069 0 286 134 129 44 955 8645 8555 8990 9080 0 2537 195 90 651 143 13579 13722 14270 14413 .96 90 0 3.83 3.924 9.062 8.846 100 100 100 100 .112 .07 8.958 9.564 1.317 14.219 15.181 9.504 9510 9930 300 52 3570 8640 47 56 232 241 3.83
16 9752 9880 0 3223 132 128 39 9890 12672 12579 12177 12270 0 3455 180 93 586 148 19967 20114 19329 19476 .97 100 0 1.014 .987 1.311 1.241 100 100 100 100 .786 .495 1.272 1.249 1.285 2.019 1.982 1.238 22469 21929 371 80 3730 8650 48 58 248 258 1.014
17 2571 2696 0 612 127 125 30 2455 19921 19832 20546 20635 0 4057 98 89 39 141 31479 31621 32613 32754 .97 110 0 3.681 3.665 8.27 8.146 100 100 100 100 .124 .078 8.078 7.991 1.28 12.823 12.685 8.088 22287 23117 352 80 3870 8650 47 58 261 272 3.681
18 11 138 0 136 127 127 32 51 133 42 11 102 0 106 98 91 39 144 67 211 17 162 .72 100 -50 .667 .999 .933 31 16 27 17 1.214 .765 .824 1 4.388 1.307 1.587 .758 93 22 328 80 4020 8640 47 57 277 287 .386
19 4231 4358 0 1711 129 127 32 4232 1459 1370 1317 1406 0 565 92 89 33 141 2175 2316 2090 2232 .96 100 0 -.961 -1.017 .335 .317 100 100 100 98 3.089 1.946 .324 .311 1.569 .514 .494 .313 5602 5548 300 80 4160 8650 48 58 291 301 -.961
20 2302 2428 0 638 129 126 32 2276 1874 1789 1776 1861 0 603 90 85 32 135 2840 2975 2819 2954 .96 110 0 .319 .292 .764 .793 100 100 100 100 1.272 .801 .786 .772 1.333 1.248 1.225 .797 4065 4078 388 80 4310 8640 46 57 305 316 .319

Total number of rows: 43008

Table truncated, full table size 9457 Kbytes.




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