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Sample GSM6275 Query DataSets for GSM6275
Status Public on Apr 15, 2004
Title AML 1
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 1
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=650650LaserPower=44.7
Lot batch = shcz083
 
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 GPL318
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
1 946 1107 0 117 206 161 153 966 1826 1622 1583 1787 0 324 357 204 442 392 3119 3512 3044 3437 .84 50 0 1.691 1.686 1.662 1.694 100 100 100 100 .596 .31 1.679 1.673 1.295 3.229 3.218 2.664 2588 2529 104 12 1890 7840 41 46 42 47 1.691
2 1490 1618 0 867 148 128 64 1303 1104 964 1024 1164 0 719 165 140 96 269 1854 2123 1969 2238 .97 60 0 .509 .402 .681 .761 96 90 78 75 1.352 .703 .74 .687 2.149 1.423 1.322 .779 2267 2514 170 32 2020 7830 40 46 55 61 .509
3 2795 2919 0 1454 156 124 150 2461 1294 1171 1200 1323 0 815 146 123 90 237 2252 2488 2308 2544 .95 60 0 -.128 -.276 .449 .489 100 93 100 87 2.102 1.093 .476 .429 1.354 .915 .826 .487 3632 3995 170 32 2170 7830 40 46 70 76 -.128
4 570 689 0 478 136 119 111 637 356 246 212 322 0 180 124 110 67 212 473 685 408 619 .87 80 0 -.429 -.483 .393 .37 90 69 80 59 2.589 1.347 .386 .372 2.355 .743 .715 .355 883 782 306 52 2320 7840 40 48 84 92 -.429
5 871 1002 0 504 151 131 95 875 703 584 426 545 0 476 130 119 56 229 1123 1352 819 1048 .88 70 0 .36 -.088 .572 .54 93 84 90 81 1.498 .779 .667 .489 1.87 1.284 .941 .747 1459 1297 213 32 2470 7830 39 46 99 106 .36
6 668 795 0 396 134 127 46 604 468 354 310 424 0 337 126 114 86 219 681 900 596 815 .84 80 0 .173 -.164 .481 .525 100 94 71 53 1.706 .887 .586 .464 1.832 1.127 .892 .705 958 978 289 52 2610 7840 40 48 113 121 .173
7 575 698 0 687 127 123 28 792 1145 1035 781 891 0 968 121 110 81 212 1990 2202 1502 1713 .95 90 0 1.329 1.385 1.354 1.315 96 86 96 82 .765 .398 1.307 1.358 2.077 2.513 2.612 1.374 1827 1356 312 52 2760 7840 39 48 127 136 1.329
8 636 761 0 536 128 125 30 734 234 127 133 240 0 95 113 107 40 206 244 450 256 462 .79 80 0 -1.588 -1.314 .186 .184 98 92 71 61 5.78 3.005 .173 .209 1.835 .333 .402 .15 861 769 254 52 2910 7840 40 48 143 151 -1.588
9 799 916 0 723 119 117 28 893 622 513 370 479 0 460 113 109 39 210 987 1196 712 921 .72 80 0 .144 -.167 .5 .489 98 96 98 84 1.741 .905 .574 .463 2.737 1.105 .891 .51 1406 1169 244 52 3050 7840 40 48 157 165 .144
10 771 886 0 394 141 115 141 700 246 133 128 241 0 84 117 113 38 217 256 473 246 463 .8 80 0 -1.453 -1.647 .179 .182 90 78 88 69 5.263 2.737 .19 .166 2.063 .365 .319 .167 833 899 265 52 3190 7830 39 47 171 179 -1.453
11 577 695 0 1569 128 118 80 1653 666 554 303 415 0 538 118 112 40 215 1065 1281 583 798 .96 90 0 -.634 .014 .304 .343 92 88 84 78 2.984 1.552 .335 .525 2.383 .645 1.01 .328 2207 880 322 52 3350 7840 39 48 186 195 -.634
12 745 861 0 1793 119 116 30 1735 1656 1546 672 782 0 1572 115 110 50 212 2973 3185 1292 1504 .95 90 0 .777 .795 .867 .847 96 96 100 98 1.122 .584 .891 .902 1.671 1.714 1.735 .866 3281 1417 312 52 3490 7840 39 48 200 209 .777
13 552 671 0 482 150 119 423 602 725 613 408 520 0 530 116 112 38 215 1179 1394 785 1000 .89 80 0 .97 .507 1.132 1.136 53 28 100 100 .982 .511 1.018 .739 2.304 1.958 1.421 1.063 1215 960 264 52 3640 7850 41 49 216 224 .97
14 773 905 0 130 205 132 672 795 352 223 206 335 0 95 131 129 49 248 429 677 396 644 .79 50 0 -.89 -.964 .25 .294 75 0 91 91 3.565 1.854 .281 .266 1.844 .539 .512 .268 1018 979 104 12 3780 7840 41 46 231 236 -.89
15 953 1072 0 623 196 119 1299 895 8991 8879 9106 9218 0 6070 124 112 137 215 17075 17290 17512 17727 .97 100 0 4.254 4.2 10.468 9.831 33 0 100 98 .101 .052 9.921 9.555 1.535 19.078 18.375 10.098 9774 10059 407 80 3930 7840 39 49 244 254 4.254
16 4317 4437 0 3005 123 120 36 4333 10553 10438 9428 9543 0 6578 138 115 108 221 20073 20294 18131 18352 .96 80 0 2.212 2.07 2.635 2.496 98 98 100 100 .415 .216 2.409 2.184 1.666 4.633 4.2 2.385 14771 13745 258 52 4070 7840 40 48 259 267 2.212
17 1521 1650 0 670 140 129 61 1285 4366 4221 5112 5257 0 2434 286 145 370 279 8117 8396 9831 10110 .94 60 0 2.659 2.692 2.988 3.134 100 96 93 90 .304 .158 3.285 3.361 1.459 6.317 6.463 3.679 5506 6633 165 32 4210 7830 40 46 274 280 2.659
18 737 857 0 320 124 120 37 706 253 138 131 246 0 73 145 115 174 221 265 487 252 473 .62 70 0 -1.412 -1.549 .201 .201 100 100 28 0 5.116 2.66 .195 .178 1.968 .376 .342 .124 844 868 224 32 4370 7840 40 47 289 296 -1.412
19 833 953 0 922 128 120 50 1039 501 386 146 261 0 422 122 115 46 221 742 963 281 502 .87 70 0 -.485 -1.569 .324 .389 100 90 87 78 2.692 1.4 .372 .175 2.292 .714 .337 .358 1425 979 213 32 4530 7840 40 47 305 312 -.485
20 998 1112 0 1100 118 114 29 1324 1104 995 507 616 0 1022 115 109 40 210 1913 2123 975 1185 .92 90 0 .531 -.034 .671 .707 100 100 100 90 1.331 .692 .752 .508 2.062 1.445 .977 .826 2319 1505 294 52 4660 7840 39 48 317 326 .531

Total number of rows: 43008

Table truncated, full table size 9600 Kbytes.




Supplementary data files not provided
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