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Sample GSM6312 Query DataSets for GSM6312
Status Public on Apr 15, 2004
Title AML 68
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 68
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=760650LaserPower=3.873.83
Lot batch = shdj079
 
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
1 505 641 0 191 209 136 529 467 422 258 262 426 0 141 214 164 321 288 453 740 460 747 .79 60 0 -.045 -.136 .499 .52 46 0 25 0 1.81 1.032 .552 .519 2.046 .969 .91 .574 725 767 167 32 1630 7840 33 39 20 26 -.045
2 6428 6569 0 2559 373 141 924 6208 988 805 651 834 0 939 219 183 294 321 1412 1733 1142 1463 .6 70 0 -2.136 -2.493 .102 .098 100 100 84 56 7.712 4.396 .13 .101 1.803 .227 .178 .17 7013 7079 214 32 1760 7840 32 39 32 39 -2.136
3 1851 1996 0 1331 193 145 249 1664 1382 1195 1161 1348 0 795 221 187 196 328 2096 2425 2037 2365 .92 50 0 .333 .138 .889 .827 91 58 100 83 1.392 .794 .718 .627 1.683 1.26 1.1 .692 2859 3012 104 12 1910 7840 33 38 48 53 .333
4 811 940 0 411 135 129 40 729 547 373 370 544 0 264 178 174 74 305 654 960 649 954 .86 60 0 -.156 -.321 .521 .516 96 96 87 75 1.954 1.114 .512 .456 2.528 .898 .8 .545 1102 1181 164 32 2060 7840 33 39 63 69 -.156
5 1523 1664 0 615 219 141 472 1621 1105 938 820 987 0 364 184 167 101 293 1646 1939 1439 1732 .63 60 0 .022 -.082 .583 .531 100 81 100 100 1.728 .985 .579 .538 1.472 1.015 .945 .275 2559 2343 164 32 2210 7830 32 38 78 84 .022
6 1014 1152 0 364 191 138 415 932 439 272 269 436 0 116 176 167 74 293 477 770 472 765 .81 70 0 -.966 -1.103 .289 .28 90 65 96 90 3.426 1.953 .292 .265 1.588 .512 .465 .27 1204 1283 212 32 2360 7840 32 39 92 99 -.966
7 909 1039 0 1394 137 130 39 1564 1407 1243 1034 1198 0 963 170 164 67 288 2181 2468 1814 2102 .93 80 0 .48 .997 1.168 .855 90 90 94 90 1.258 .717 .795 1.138 3.232 1.394 1.996 .72 2807 1943 269 52 2500 7840 32 40 106 114 .48
8 774 909 0 430 148 135 67 810 340 176 157 321 0 104 167 164 63 288 309 596 275 563 .69 60 0 -1.391 -1.491 .244 .212 96 96 87 71 4.602 2.623 .217 .203 3.03 .381 .356 .199 986 931 165 32 2640 7830 32 38 121 127 -1.391
9 475 609 0 272 140 134 51 424 377 214 237 400 0 149 166 163 64 286 375 661 416 702 .69 90 0 -.175 -.192 .553 .568 80 80 80 76 1.981 1.129 .505 .499 1.843 .885 .875 .457 638 712 338 52 2790 7840 31 40 134 143 -.175
10 287 423 0 105 138 136 34 255 358 197 188 349 0 128 166 161 69 282 346 628 330 612 .57 60 0 .439 .201 .791 .759 96 93 84 71 1.294 .738 .773 .655 2.818 1.355 1.149 .952 452 475 158 32 2940 7840 33 39 151 157 .439
11 4395 4528 0 2141 137 133 40 4645 732 565 470 637 0 301 172 167 69 293 991 1284 825 1118 .85 90 0 -2.228 -2.414 .124 .128 100 100 98 94 8.221 4.686 .122 .107 1.977 .213 .188 .108 5210 4865 328 52 3080 7840 31 40 163 172 -2.228
12 8329 8464 0 3691 141 135 51 8080 6390 6228 5711 5873 0 2771 169 162 95 284 10926 11211 10019 10304 .96 90 0 .435 .267 .798 .746 100 100 100 100 1.297 .739 .771 .686 1.545 1.352 1.203 .751 14308 14040 324 52 3230 7830 30 39 178 187 .435
13 1324 1463 0 585 145 139 52 1227 880 725 755 910 0 320 169 155 102 272 1272 1544 1325 1596 .89 80 0 .052 .001 .657 .632 100 96 100 94 1.692 .965 .591 .57 2.04 1.037 1 .532 1952 2079 256 52 3380 7830 31 39 194 202 .052
14 349 484 0 213 145 135 107 342 691 528 515 678 0 246 175 163 125 286 926 1212 904 1189 .81 110 0 1.438 1.372 1.591 1.567 82 75 97 88 .648 .369 1.544 1.476 1.982 2.709 2.589 1.608 870 864 441 80 3530 7830 29 40 207 218 1.438
15 1456 1589 0 718 139 133 42 1368 840 683 713 870 0 320 163 157 66 275 1198 1474 1251 1526 .84 80 0 -.191 -.219 .576 .481 90 90 98 90 2.003 1.142 .499 .49 2.615 .876 .859 .419 2051 2169 236 52 3670 7830 31 39 223 231 -.191
16 7145 7277 0 3222 142 132 64 6933 10371 10214 10797 10954 0 3805 192 157 225 275 17919 18195 18942 19218 .92 110 0 1.37 1.407 1.635 1.406 100 100 100 100 .679 .387 1.473 1.511 1.898 2.585 2.651 1.44 17147 17942 426 80 3820 7840 30 41 236 247 1.37
17 1739 1870 0 1281 142 131 62 1618 13418 13260 15648 15806 0 8113 194 158 235 277 23263 23540 27453 27730 .88 110 0 3.846 3.981 7.97 7.614 83 81 97 95 .122 .07 8.195 8.998 1.952 14.378 15.786 8.235 14878 17387 377 80 3970 7830 29 40 251 262 3.846
18 -2 129 0 134 137 131 35 25 195 42 22 175 0 114 166 153 66 268 74 342 39 307 .43 100 -50 1.144 1.093 23 11 25 6 .595 .339 1.68 4.401 2.947 1.108 67 20 323 80 4110 7830 30 40 266 276 1.559
19 3915 4044 0 1983 133 129 37 3606 1476 1317 1294 1453 0 652 171 159 71 279 2311 2589 2270 2549 .93 100 0 -.642 -.786 .407 .335 93 93 98 97 2.738 1.561 .365 .331 2.507 .641 .58 .332 4923 5209 308 80 4260 7830 30 40 281 291 -.642
20 1905 2035 0 760 136 130 40 1943 1074 911 909 1072 0 382 172 163 69 286 1598 1884 1595 1881 .91 110 0 -.282 -.256 .455 .477 100 100 100 97 2.133 1.216 .469 .477 1.566 .823 .837 .455 2854 2814 372 80 4400 7840 30 41 294 305 -.282

Total number of rows: 43008

Table truncated, full table size 9366 Kbytes.




Supplementary data files not provided
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