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Sample GSM6269 Query DataSets for GSM6269
Status Public on Apr 15, 2004
Title AML 113
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 113
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=640650LaserPower=4.094.63
Lot batch = shcz078
 
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
1 173 295 0 181 167 122 706 207 375 262 219 332 0 165 170 113 602 128 298 426 249 377 .83 100 0 .524 .525 1.455 1.314 5 0 5 0 .79 .695 1.266 1.266 2.42 1.438 1.439 2.085 469 392 422 80 1780 7730 36 46 25 35 .524
2 2376 2498 0 1518 137 122 142 2539 6593 6478 5756 5871 0 3802 159 115 435 131 7361 7492 6541 6672 .97 90 0 1.536 1.461 2.771 2.543 94 92 100 98 .392 .345 2.551 2.423 1.497 2.899 2.753 2.568 9017 8132 276 52 1920 7720 35 44 39 48 1.536
3 1117 1240 0 701 125 123 32 1193 904 795 771 880 0 390 114 109 33 124 903 1027 876 1000 .96 90 0 -.401 -.35 .703 .643 98 98 100 100 1.501 1.321 .666 .69 1.451 .757 .784 .617 1988 1888 289 52 2070 7720 35 44 54 63 -.401
4 341 461 0 234 125 120 31 372 307 198 157 266 0 119 113 109 34 124 225 349 178 302 .82 90 0 -.725 -.935 .543 .509 94 90 98 92 1.879 1.653 .532 .46 2.397 .605 .523 .476 570 498 298 52 2210 7730 36 45 68 77 -.725
5 299 423 0 186 130 124 33 328 241 131 125 235 0 69 116 110 34 125 149 274 142 267 .69 90 0 -1.14 -1.074 .404 .427 98 94 92 84 2.504 2.203 .399 .418 2.114 .454 .475 .314 459 424 313 52 2360 7720 35 44 83 92 -1.14
6 244 367 0 176 128 123 31 257 238 129 116 225 0 94 116 109 34 124 147 270 132 256 .73 80 0 -.81 -.888 .533 .453 92 88 86 76 1.992 1.753 .502 .475 2.585 .57 .54 .439 386 360 240 52 2510 7730 37 45 99 107 -.81
7 326 452 0 269 127 126 32 378 438 327 268 379 0 202 116 111 33 126 372 498 305 431 .86 80 0 -.025 -.098 .95 .889 98 94 100 98 1.156 1.017 .865 .822 1.698 .983 .934 .8 705 594 264 52 2660 7720 36 44 114 122 -.025
8 199 321 0 121 127 122 32 221 163 47 32 148 0 55 117 116 33 132 53 185 36 168 .4 80 0 -2.049 -2.452 .18 .206 94 90 50 30 4.702 4.138 .213 .161 3.658 .242 .183 .18 268 231 272 52 2800 7720 36 44 128 136 -2.049
9 74 196 0 59 129 122 35 79 318 198 170 290 0 120 125 120 41 136 225 361 193 330 .67 80 0 1.51 1.384 2.371 2.241 78 53 98 80 .399 .351 2.506 2.297 1.783 2.848 2.611 2.838 277 244 264 52 2940 7720 36 44 142 150 1.51
10 226 353 0 120 128 127 32 228 156 42 28 142 0 61 119 114 40 130 48 177 32 161 .17 90 0 -2.256 -2.828 .22 .194 96 90 40 19 5.429 4.777 .184 .124 4.809 .209 .141 .087 270 254 337 52 3090 7720 35 44 156 165 -2.256
11 347 473 0 169 130 126 34 338 173 63 60 170 0 41 113 110 30 125 72 197 68 193 .48 70 0 -2.239 -2.347 .16 .177 96 96 78 50 5.365 4.721 .186 .173 2.41 .212 .196 .128 401 407 214 32 3240 7710 35 42 172 179 -2.239
12 555 679 0 583 129 124 35 677 689 578 460 571 0 409 115 111 32 126 657 783 523 649 .91 90 0 -.044 -.086 1.004 .869 94 92 100 100 1.171 1.031 .854 .829 1.714 .97 .942 .826 1255 1015 328 52 3380 7730 36 45 185 194 -.044
13 294 416 0 273 128 122 33 329 367 252 248 363 0 128 117 115 34 131 286 417 282 413 .87 80 0 -.2 -.061 .974 .775 88 80 98 94 1.306 1.149 .766 .844 2.059 .87 .959 .618 581 542 267 52 3540 7730 37 45 202 210 -.2
14 21 153 0 91 138 132 39 48 201 80 85 206 0 51 126 121 41 138 91 228 97 234 .42 50 0 .921 2.201 1.574 .819 41 33 75 58 .6 .528 1.667 4.048 3.918 1.894 4.6 1.079 128 106 94 12 3670 7750 40 45 216 221 .921
15 329 452 0 274 127 123 32 340 2478 2362 2018 2134 0 1650 118 116 35 132 2684 2816 2293 2425 .94 100 0 2.981 2.801 8.057 6.954 82 77 100 98 .144 .127 6.947 6.134 2.029 7.894 6.97 6.864 2702 2347 409 80 3820 7720 35 45 229 239 2.981
16 2293 2416 0 1637 128 123 60 2165 4113 3996 4314 4431 0 2524 120 117 36 133 4541 4674 4902 5035 .96 100 0 1.069 1.096 2.332 1.84 97 92 100 100 .542 .477 1.846 1.881 1.943 2.097 2.138 1.751 6161 6607 354 80 3970 7730 36 46 244 254 1.069
17 534 657 0 464 127 123 33 576 3642 3525 3300 3417 0 2003 118 117 33 133 4006 4139 3750 3883 .89 100 0 2.798 2.812 7.071 6.295 91 86 100 100 .163 .144 6.12 6.18 1.846 6.954 7.022 5.924 4101 3834 347 80 4120 7730 36 46 259 269 2.798
18 58 178 0 61 125 120 35 69 149 31 21 139 0 58 119 118 33 134 35 169 24 158 .03 70 0 -.97 -1.281 .745 .904 68 43 40 25 2.226 1.959 .449 .362 3.372 .511 .411 .051 100 79 184 32 4260 7740 38 45 274 281 -.97
19 179 302 0 249 127 123 35 229 189 77 75 187 0 56 115 112 32 127 88 215 85 213 .54 100 0 -1.388 -1.071 .432 .391 90 76 78 53 2.974 2.617 .336 .419 3.078 .382 .476 .174 306 254 362 80 4410 7730 36 46 288 298 -1.388
20 295 419 0 198 129 124 35 289 246 129 117 234 0 80 124 117 43 133 147 280 133 266 .61 80 0 -.979 -1.15 .517 .418 94 84 82 67 2.24 1.971 .446 .397 2.527 .507 .451 .345 418 412 243 52 4550 7720 36 44 303 311 -.979

Total number of rows: 43008

Table truncated, full table size 9171 Kbytes.




Supplementary data files not provided
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