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Sample GSM6306 Query DataSets for GSM6306
Status Public on Apr 15, 2004
Title AML 61
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 61
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=670650LaserPower=3.894.1
Lot batch = shdj073
 
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
1 244 353 0 174 123 109 158 234 1504 1412 1350 1442 0 764 165 92 941 96 1471 1567 1406 1502 .84 80 0 2.652 2.527 7.581 6.278 59 36 67 26 .166 .159 6.034 5.533 2.374 6.286 5.763 6.055 1646 1594 267 52 1580 8460 26 34 22 30 2.652
2 2194 2302 0 1152 110 108 28 2077 995 904 900 991 0 545 97 91 33 95 942 1036 938 1032 .84 80 0 -1.141 -1.227 .428 .408 100 100 96 94 2.298 2.206 .435 .41 2.816 .453 .427 .399 2981 3094 274 52 1730 8450 25 33 37 45 -1.141
3 916 1024 0 653 111 108 28 912 864 772 736 828 0 502 94 92 34 96 804 900 767 863 .88 70 0 -.182 -.257 .934 .857 93 90 96 96 1.181 1.134 .846 .803 1.968 .882 .837 .788 1684 1652 206 32 1880 8450 25 32 52 59 -.182
4 389 496 0 262 111 107 26 401 376 284 248 340 0 202 92 92 31 96 296 392 258 354 .83 80 0 -.439 -.591 .666 .622 98 96 90 86 1.412 1.355 .708 .638 2.49 .738 .664 .696 685 637 254 52 2020 8450 25 33 66 74 -.439
5 775 888 0 553 116 113 26 874 1060 963 886 983 0 642 99 97 35 101 1003 1104 923 1024 .84 80 0 .199 .252 1.058 1.106 98 96 100 94 .908 .871 1.102 1.143 2.826 1.148 1.191 1.151 1837 1661 266 52 2170 8450 25 33 81 89 .199
6 617 735 0 292 119 118 28 584 1071 978 1019 1112 0 431 96 93 29 97 1019 1116 1061 1158 .81 60 0 .803 .783 1.779 1.73 93 90 100 100 .597 .573 1.675 1.652 2.842 1.744 1.72 1.776 1562 1636 164 32 2310 8450 26 32 96 102 .803
7 1626 1758 0 434 154 132 154 1486 3710 3590 4197 4317 0 1255 194 120 264 125 3740 3865 4372 4497 .64 50 0 1.331 1.427 2.366 2.454 100 100 100 100 .414 .397 2.416 2.581 2.112 2.517 2.689 3.313 5076 5823 104 12 2460 8450 26 31 111 116 1.331
8 394 514 0 174 123 120 31 448 313 213 216 316 0 114 109 100 55 104 222 326 225 329 .77 70 0 -1.014 -.808 .46 .525 100 100 96 78 2.103 2.019 .475 .548 1.695 .495 .571 .445 661 610 225 32 2600 8440 24 31 124 131 -1.014
9 348 466 0 120 118 118 30 360 698 602 592 688 0 290 100 96 34 100 627 727 617 717 .86 90 0 .801 .825 1.529 1.66 100 100 98 96 .598 .574 1.672 1.701 1.827 1.742 1.772 1.858 962 940 340 52 2750 8440 23 32 138 147 .801
10 267 385 0 126 122 118 33 281 220 122 107 205 0 89 101 98 34 102 127 229 111 214 .66 60 0 -1.145 -1.26 .367 .43 96 96 87 68 2.303 2.211 .434 .401 2.315 .452 .417 .427 403 374 164 32 2890 8440 25 31 154 160 -1.145
11 3364 3484 0 1168 124 120 30 3367 503 400 385 488 0 194 106 103 35 107 417 524 401 508 .9 90 0 -3.014 -3.068 .117 .129 100 100 98 98 8.418 8.081 .119 .114 1.466 .124 .119 .113 3767 3749 329 52 3040 8450 24 33 167 176 -3.014
12 3514 3632 0 3453 119 118 27 4375 5740 5637 5119 5222 0 4154 107 103 33 107 5872 5979 5332 5440 .91 100 0 .425 .602 1.437 1.288 97 96 100 100 .776 .745 1.288 1.457 3.178 1.342 1.517 1.273 10012 8633 360 80 3190 8450 24 34 182 192 .425
13 665 784 0 460 121 119 29 705 1327 1220 1067 1174 0 878 110 107 33 111 1271 1382 1111 1223 .88 100 0 .85 .741 1.655 1.833 96 95 98 98 .578 .555 1.73 1.605 2.27 1.803 1.671 1.935 1925 1732 313 80 3340 8450 24 34 197 207 .85
14 237 356 0 122 121 119 31 239 396 294 294 396 0 169 107 102 57 106 306 413 306 413 .79 120 0 .358 .37 1.176 1.259 95 90 91 80 .813 .78 1.23 1.241 2.328 1.281 1.292 1.361 533 531 453 120 3480 8450 23 35 210 222 .358
15 793 913 0 288 122 120 32 721 8497 8388 9431 9540 0 3237 132 109 196 114 8738 8851 9824 9938 .89 90 0 3.599 3.631 11.279 11.971 96 94 100 100 .086 .083 11.634 11.893 1.697 12.119 12.388 12.888 9109 10224 250 52 3620 8440 23 32 225 234 3.599
16 3371 3487 0 2252 118 116 30 3206 6679 6574 6550 6655 0 4534 119 105 147 109 6848 6957 6823 6932 .86 120 0 1.095 1.017 2.011 1.897 97 94 96 94 .488 .468 2.051 1.943 3.309 2.136 2.024 2.242 9780 9921 457 120 3770 8450 23 35 239 251 1.095
17 1647 1758 0 715 116 111 42 1402 7242 7143 7929 8028 0 3148 104 99 35 103 7441 7544 8259 8363 .88 120 0 2.408 2.326 5.306 5.292 95 91 100 100 .196 .188 5.095 4.814 2.115 5.307 5.015 5.532 8545 9576 403 120 3920 8450 23 35 254 266 2.408
18 19 129 0 97 113 110 44 36 119 23 3 99 0 75 101 96 34 100 24 124 3 103 .46 100 -50 -2.604 1.048 .984 22 8 27 12 1.565 1.503 .639 .158 3.139 .666 .164 .52 59 22 307 80 4060 8440 23 33 269 279 -.587
19 2343 2454 0 1194 112 111 27 2160 1459 1364 1373 1468 0 759 99 95 32 99 1421 1520 1430 1529 .92 100 0 -.604 -.712 .698 .614 100 98 100 100 1.584 1.52 .631 .586 2.119 .658 .61 .609 3524 3716 306 80 4210 8450 24 34 284 294 -.604
20 1541 1655 0 486 116 114 27 1521 1609 1518 1498 1589 0 589 96 91 32 95 1581 1676 1560 1655 .89 110 0 .056 .018 .968 1.007 100 100 100 100 1.002 .962 .998 .972 1.662 1.04 1.013 1.044 3039 3039 378 80 4350 8440 22 33 297 308 .056

Total number of rows: 43008

Table truncated, full table size 9329 Kbytes.




Supplementary data files not provided

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