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Sample GSM6325 Query DataSets for GSM6325
Status Public on Apr 15, 2004
Title AML 75
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 75
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=4.494.56
Lot batch = shdj092
 
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
1 387 506 0 295 122 119 28 454 1834 1722 1687 1799 0 1008 117 112 36 124 1913 2038 1874 1999 .96 90 0 2.075 2.276 4.328 4.038 94 90 100 100 .264 .237 3.793 4.359 1.755 4.214 4.844 3.795 2176 2074 332 52 1630 8340 29 38 18 27 2.075
2 5467 5583 0 2480 119 116 27 4971 5224 5111 5478 5591 0 2396 119 113 38 126 5679 5804 6087 6212 .98 90 0 .192 .155 1.065 1.032 100 100 100 100 .973 .875 1.028 1.002 1.306 1.142 1.113 1.015 10082 10945 325 52 1780 8340 29 38 33 42 .192
3 1207 1322 0 1459 120 115 32 1635 1114 1000 688 802 0 823 122 114 41 127 1111 1238 764 891 .97 60 0 -.557 -.659 .646 .587 93 93 93 93 1.635 1.472 .612 .57 1.489 .68 .633 .576 2635 1895 164 32 1930 8350 32 38 50 56 -.557
4 747 870 0 556 160 123 344 778 2288 2171 2029 2146 0 1382 133 117 97 130 2412 2542 2254 2384 .97 90 0 1.633 1.594 3.242 2.906 69 53 100 100 .358 .323 2.79 2.716 1.54 3.101 3.018 2.684 2949 2776 289 52 2080 8340 29 38 63 72 1.633
5 1973 2092 0 1166 156 119 338 1928 2691 2569 2448 2570 0 1481 133 122 96 136 2854 2990 2720 2856 .97 90 0 .566 .463 1.415 1.332 88 80 100 98 .75 .675 1.332 1.241 1.59 1.481 1.379 1.32 4497 4421 300 52 2210 8340 29 38 76 85 .566
6 1311 1432 0 467 124 121 27 1236 2312 2192 2308 2428 0 918 122 120 39 133 2436 2569 2564 2698 .97 70 0 .979 .968 1.754 1.846 100 100 100 100 .564 .507 1.773 1.76 1.271 1.971 1.956 1.84 3428 3619 218 32 2360 8340 30 37 92 99 .979
7 1929 2050 0 1393 121 121 28 2051 3578 3457 3441 3562 0 1831 122 121 37 134 3841 3976 3823 3958 .98 90 0 .905 .987 2.175 1.798 96 96 100 100 .593 .534 1.686 1.784 1.95 1.873 1.982 1.569 5508 5370 321 52 2520 8340 29 38 107 116 .905
8 612 730 0 458 120 118 29 672 362 245 227 344 0 157 122 117 37 130 272 402 252 382 .9 80 0 -1.304 -1.279 .401 .397 100 96 94 86 2.743 2.469 .365 .371 1.522 .405 .412 .339 917 839 233 52 2650 8350 31 39 121 129 -1.304
9 577 695 0 290 120 118 29 551 611 492 472 591 0 282 121 119 39 132 547 679 524 657 .93 100 0 -.011 -.138 .869 .941 100 97 97 96 1.12 1.008 .893 .818 1.553 .992 .909 .908 1043 1049 387 80 2800 8340 29 39 135 145 -.011
10 439 554 0 179 117 115 29 421 380 258 224 346 0 137 125 122 39 136 287 422 249 384 .82 70 0 -.554 -.819 .58 .636 100 100 100 93 1.632 1.469 .613 .51 1.743 .681 .567 .596 679 663 192 32 2950 8340 30 37 151 158 -.554
11 5158 5273 0 2896 118 115 28 5281 953 836 823 940 0 488 122 117 38 130 929 1059 914 1044 .96 100 0 -2.507 -2.496 .159 .157 100 100 100 98 6.317 5.685 .158 .16 1.55 .176 .177 .155 6117 5981 378 80 3090 8340 29 39 164 174 -2.507
12 7048 7165 0 6680 119 117 27 8589 9616 9500 8002 8118 0 6849 121 116 41 129 10556 10684 8891 9020 .99 100 0 .297 .335 1.348 1.107 100 98 100 100 .904 .814 1.106 1.135 1.805 1.229 1.262 1.068 18089 15050 358 80 3240 8340 29 39 179 189 .297
13 1093 1210 0 750 119 117 26 1221 1958 1843 1582 1697 0 1189 121 115 42 128 2048 2176 1758 1886 .97 110 0 .746 .685 1.595 1.516 96 95 100 98 .663 .596 1.509 1.447 1.695 1.677 1.608 1.554 3064 2675 356 80 3390 8350 29 40 193 204 .746
14 396 512 0 185 119 116 28 393 763 648 608 723 0 315 121 115 44 128 720 848 676 803 .93 120 0 .873 .771 1.637 1.629 98 98 100 100 .606 .546 1.649 1.535 1.528 1.832 1.706 1.728 1041 1004 441 120 3530 8340 28 40 207 219 .873
15 1014 1129 0 571 119 115 29 1017 8309 8189 8871 8991 0 4151 124 120 52 133 9099 9232 9857 9990 .98 100 0 3.161 3.281 8.634 7.98 97 96 100 100 .124 .112 8.052 8.749 1.473 8.947 9.721 7.961 9206 9885 309 80 3670 8340 29 39 222 232 3.161
16 5533 5648 0 3679 118 115 28 5496 15520 15402 13330 13448 0 9572 125 118 49 131 17113 17244 14811 14942 .98 120 0 1.639 1.421 3.321 2.79 96 95 100 100 .357 .321 2.802 2.409 1.818 3.114 2.677 2.75 20898 18863 417 120 3830 8350 29 41 237 249 1.639
17 2698 2813 0 1111 119 115 40 2518 20437 20320 22611 22728 0 8558 127 117 58 130 22578 22708 25123 25253 .99 120 0 3.165 3.219 8.338 8.023 100 99 100 100 .124 .112 8.07 8.381 1.241 8.967 9.312 8.045 22838 25309 394 120 3970 8340 28 40 251 263 3.165
18 9 122 0 115 117 113 33 49 182 66 37 153 0 122 121 116 39 129 73 202 41 170 .76 100 -50 2.192 1.577 1.28 30 20 46 21 .742 .668 1.347 4.111 3.563 1.497 4.568 1.131 115 46 331 80 4110 8330 28 38 266 276 .582
19 4819 4938 0 1700 142 119 195 4664 2204 2085 2153 2272 0 737 136 119 103 132 2317 2449 2392 2524 .98 90 0 -1.01 -1.01 .45 .456 100 100 100 100 2.237 2.013 .447 .447 1.211 .497 .496 .438 6749 6972 262 52 4260 8330 28 37 281 290 -1.01
20 2143 2259 0 857 132 116 155 1935 1960 1840 2036 2156 0 721 131 120 84 133 2044 2178 2262 2396 .97 120 0 .079 .078 1.01 .96 98 95 100 100 1.052 .946 .951 .95 1.521 1.057 1.056 .917 3775 4179 425 120 4410 8340 28 40 295 307 .079

Total number of rows: 43008

Table truncated, full table size 9442 Kbytes.




Supplementary data files not provided
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