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Sample GSM6280 Query DataSets for GSM6280
Status Public on Apr 15, 2004
Title AML 12
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 12
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=710640LaserPower=4.214.43
Lot batch = shcz224
 
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 28 69 0 41 44 41 14 41 1047 1004 918 961 0 780 48 43 26 55 1287 1342 1177 1232 .82 110 0 4.972 5.393 22.617 22.139 60 48 100 98 .041 .032 24.488 32.786 2.009 31.395 42.033 25.15 1045 946 507 80 2050 7930 59 70 19 30 4.972
2 688 729 0 482 43 41 12 665 129 87 60 102 0 87 47 42 18 54 112 165 77 131 .8 90 0 -2.576 -3.161 .124 .125 94 94 73 59 7.644 5.962 .131 .087 2.907 .168 .112 .125 752 748 288 52 2200 7930 60 69 35 44 -2.576
3 238 281 0 273 44 43 12 317 184 138 78 124 0 127 49 46 17 59 177 236 100 159 .92 80 0 -.841 -1.251 .5 .47 92 88 82 71 2.297 1.792 .435 .328 2.641 .558 .42 .43 455 316 263 52 2350 7930 61 69 51 59 -.841
4 145 188 0 74 46 43 14 131 77 29 22 70 0 29 51 48 20 62 37 99 28 90 .52 60 0 -1.817 -2.362 .239 .242 87 87 50 31 4.517 3.523 .221 .152 4.269 .284 .195 .194 160 167 170 32 2500 7920 61 67 67 73 -1.817
5 171 215 0 100 48 44 17 149 353 306 251 298 0 233 52 47 22 60 392 453 322 382 .86 60 0 1.397 .912 2.256 1.953 87 81 87 81 .487 .38 2.054 1.468 2.009 2.633 1.882 2.417 455 422 160 32 2640 7910 60 66 81 87 1.397
6 124 166 0 73 44 42 12 120 124 77 76 123 0 64 51 47 21 60 99 159 97 158 .77 60 0 -.282 -.348 .533 .587 93 87 75 65 1.558 1.216 .642 .613 2.548 .823 .786 .714 197 200 164 32 2790 7910 60 66 96 102 -.282
7 120 162 0 136 44 42 14 165 389 343 250 296 0 272 50 46 20 59 440 499 321 379 .92 90 0 1.414 1.417 2.102 1.914 90 84 96 92 .481 .375 2.079 2.083 2.403 2.665 2.671 2.127 508 370 333 52 2930 7910 58 67 108 117 1.414
8 83 125 0 72 44 42 13 85 92 48 44 88 0 50 50 44 20 56 62 118 56 113 .58 80 0 -.466 -.557 .59 .693 80 75 65 53 1.771 1.381 .565 .53 2.828 .724 .68 .529 133 127 296 52 3080 7910 59 67 124 132 -.466
9 100 144 0 49 46 44 12 103 113 63 61 111 0 26 52 50 18 64 81 145 78 142 .56 50 0 -.351 -.355 .626 .641 100 100 100 83 1.635 1.275 .612 .61 2.026 .784 .782 .448 166 161 92 12 3230 7900 59 64 140 145 -.351
10 93 135 0 66 44 42 14 91 80 33 30 77 0 32 52 47 20 60 42 103 38 99 .39 90 0 -1.105 -1.274 .321 .31 82 75 55 36 2.758 2.151 .363 .323 3.364 .465 .414 .264 124 123 352 52 3370 7910 58 67 152 161 -1.105
11 727 771 0 310 52 44 35 650 178 133 138 183 0 77 50 45 19 58 171 228 177 235 .85 60 0 -1.931 -2.039 .211 .195 93 90 87 87 4.887 3.812 .205 .19 2.177 .262 .243 .189 783 865 164 32 3520 7900 59 65 169 175 -1.931
12 138 179 0 421 43 41 10 358 324 278 125 171 0 310 50 46 19 59 356 415 160 219 .97 80 -100 .216 .852 .759 92 92 88 84 1.288 1.004 .777 .906 1.922 .996 1.161 .743 636 263 270 52 3660 7900 58 66 182 190 -.006
13 192 233 0 121 43 41 11 185 496 449 458 505 0 315 52 47 21 60 576 636 587 647 .92 70 0 1.638 1.613 2.176 2.192 93 90 93 93 .412 .321 2.427 2.385 2.267 3.112 3.058 2.638 634 650 208 32 3800 7900 58 65 196 203 1.638
14 6 47 0 25 43 41 11 13 70 23 18 65 0 35 51 47 20 60 29 90 23 83 .27 100 -50 1.943 1.379 1.133 37 23 45 25 .565 .441 1.769 3 3.317 2.268 3.846 4.095 36 24 397 80 3960 7900 57 67 211 221 1.182
15 55 97 0 62 44 42 13 71 3729 3682 3771 3818 0 2702 51 47 19 60 4721 4781 4835 4895 .93 110 0 6.055 6.458 44.044 46.855 76 67 100 100 .019 .015 51.859 68.564 1.717 66.486 87.902 50.953 3753 3826 445 80 4100 7900 56 67 224 235 6.055
16 1512 1555 0 695 45 43 11 1209 2201 2151 2435 2485 0 1145 53 50 19 64 2758 2822 3122 3186 .97 90 0 1.19 1.046 2.23 1.867 98 96 100 100 .562 .438 1.779 1.61 1.923 2.281 2.065 1.757 3360 3947 303 52 4250 7890 56 65 240 249 1.19
17 56 99 0 161 45 43 10 150 2398 2350 1118 1166 0 2303 52 48 19 62 3013 3074 1433 1495 .96 100 0 4.328 4.678 15.633 15.735 78 73 100 100 .064 .05 15.667 19.964 1.616 20.085 25.595 15.476 2500 1174 398 80 4390 7890 56 66 254 264 4.328
18 90 137 0 38 58 47 38 105 73 20 14 67 0 21 56 53 22 68 26 94 18 86 .44 50 0 -2.034 -2.326 .138 .125 100 66 41 16 5.25 4.095 .19 .156 3.02 .244 .199 .225 125 104 97 12 4520 7890 58 63 269 274 -2.034
19 260 308 0 319 62 48 82 392 228 178 176 226 0 132 55 50 22 64 228 292 226 290 .86 70 0 -.781 -.204 .461 .473 78 62 96 75 2.202 1.718 .454 .677 2.003 .582 .868 .376 570 436 230 32 4660 7880 56 63 282 289 -.781
20 462 510 0 176 53 48 22 451 193 138 140 195 0 90 56 55 22 71 177 247 179 250 .81 50 0 -1.35 -1.364 .29 .332 100 100 91 91 3.268 2.549 .306 .303 1.823 .392 .389 .319 589 602 98 12 4820 7880 57 62 299 304 -1.35

Total number of rows: 43008

Table truncated, full table size 8604 Kbytes.




Supplementary data files not provided
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