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Sample GSM6264 Query DataSets for GSM6264
Status Public on Apr 15, 2004
Title AML 53
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 53
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=690650LaserPower=3.664.75
Lot batch = shcz067
 
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
1 173 303 0 107 133 130 35 203 622 510 431 543 0 203 116 112 39 187 850 1037 718 905 .81 90 0 2.066 2.054 2.75 2.686 98 92 100 100 .398 .239 2.512 2.491 1.848 4.187 4.152 2.625 713 604 356 52 1830 8370 28 37 34 43 2.066
2 1653 1780 0 944 131 127 35 1642 401 284 257 374 0 161 121 117 39 195 473 668 428 623 .9 90 0 -1.795 -1.948 .175 .171 100 100 92 90 5.782 3.469 .173 .155 1.696 .288 .259 .16 1926 1910 301 52 1980 8370 28 37 49 58 -1.795
3 495 619 0 312 127 124 29 546 243 123 123 243 0 85 123 120 41 200 205 405 205 405 .75 80 0 -1.413 -1.272 .21 .233 100 100 84 59 4.439 2.663 .225 .248 2.042 .375 .414 .207 669 618 277 52 2120 8370 29 37 64 72 -1.413
4 257 386 0 129 130 129 30 256 168 51 48 165 0 61 119 117 39 195 85 280 80 275 .34 80 0 -1.591 -1.684 .23 .252 98 98 59 23 5.02 3.012 .199 .187 2.939 .332 .311 .146 307 305 266 52 2270 8370 29 37 79 87 -1.591
5 116 245 0 66 129 129 31 108 180 67 46 159 0 66 119 113 44 188 112 300 77 265 .37 90 0 .048 -.597 .499 .488 86 78 53 32 1.612 .967 .62 .397 2.559 1.034 .661 .858 175 162 256 52 2410 8370 28 37 92 101 .048
6 110 237 0 89 130 127 28 114 203 87 75 191 0 65 120 116 44 193 145 338 125 318 .49 80 0 .347 .184 .661 .594 78 73 78 42 1.31 .786 .763 .682 2.707 1.272 1.136 .704 201 185 263 52 2550 8370 29 37 107 115 .347
7 153 278 0 116 127 125 29 179 227 112 89 204 0 85 119 115 39 192 187 378 148 340 .59 90 0 .061 -.045 .635 .643 94 88 86 65 1.598 .959 .626 .582 2.11 1.043 .969 .604 291 242 322 52 2710 8370 28 37 122 131 .061
8 168 295 0 83 130 127 30 187 175 68 67 174 0 55 114 107 37 178 113 292 112 290 .42 80 0 -.722 -.589 .354 .442 98 94 67 36 2.75 1.65 .364 .399 2.839 .606 .665 .332 255 235 276 52 2850 8370 29 37 137 145 -.722
9 94 221 0 55 129 127 29 88 163 44 46 165 0 45 123 119 39 198 73 272 77 275 .24 60 0 -.263 -.294 .524 .518 81 68 53 21 2 1.2 .5 .489 3.156 .833 .816 .505 132 140 159 32 3010 8370 30 36 154 160 -.263
10 178 306 0 107 131 128 31 192 149 28 24 145 0 47 124 121 37 202 47 248 40 242 .33 110 0 -2.041 -2.154 .206 .222 91 88 41 13 6.857 4.114 .146 .135 2.234 .243 .225 .152 220 202 432 80 3150 8380 28 39 165 176 -2.041
11 107 233 0 101 129 126 29 132 166 48 37 155 0 63 118 118 38 197 80 277 62 258 .5 80 0 -.722 -.795 .449 .493 84 73 46 25 2.75 1.65 .364 .346 2.54 .606 .576 .454 180 144 252 52 3300 8370 29 37 182 190 -.722
12 242 370 0 199 129 128 31 273 248 132 108 224 0 87 117 116 36 193 220 413 180 373 .75 80 0 -.311 -.427 .531 .484 92 90 98 71 2.068 1.241 .484 .446 2.721 .806 .744 .385 405 350 270 52 3430 8370 29 37 195 203 -.311
13 301 427 0 95 132 126 36 290 292 173 168 287 0 82 122 119 39 198 288 487 280 478 .73 70 0 -.008 -.104 .588 .65 100 100 96 90 1.676 1.006 .597 .558 1.657 .994 .93 .515 463 469 224 32 3590 8370 29 36 211 218 -.008
14 94 221 0 64 134 127 58 104 213 98 87 202 0 64 121 115 40 192 163 355 145 337 .45 70 0 .651 .625 .924 .857 81 34 81 53 1.061 .637 .942 .926 2.238 1.571 1.543 1.175 202 181 212 32 3740 8380 30 37 226 233 .651
15 160 287 0 77 134 127 47 151 1850 1728 1512 1634 0 981 124 122 39 203 2880 3083 2520 2723 .7 100 0 4.253 3.977 11.307 11.355 91 76 100 100 .087 .052 11.444 9.45 1.838 19.073 15.75 14.614 1879 1672 406 80 3880 8370 28 38 239 249 4.253
16 910 1041 0 474 134 131 33 1031 1305 1187 1012 1130 0 496 121 118 41 197 1978 2175 1687 1883 .96 90 0 .94 .89 1.167 1.123 100 100 100 100 .869 .521 1.151 1.112 1.284 1.919 1.853 1.141 2218 1922 300 52 4020 8370 28 37 253 262 .94
17 366 498 0 237 137 132 47 381 2465 2348 1831 1948 0 1580 123 117 42 195 3913 4108 3052 3247 .87 110 0 3.361 3.06 6.08 5.835 95 87 100 100 .162 .097 6.163 5.003 1.553 10.271 8.338 6.894 2729 2197 451 80 4170 8370 27 38 267 278 3.361
18 157 287 0 88 141 130 66 166 189 65 65 189 0 54 126 124 40 207 108 315 108 315 .41 60 0 -.616 -.535 .48 .489 84 62 68 40 2.554 1.532 .392 .414 2.444 .653 .69 .284 231 222 159 32 4320 8380 31 37 285 291 -.616
19 210 347 0 111 142 137 37 213 204 83 74 195 0 66 123 121 38 202 138 340 123 325 .47 70 0 -.623 -.768 .363 .335 96 96 68 46 2.566 1.54 .39 .352 2.172 .649 .587 .351 296 284 220 32 4470 8360 28 35 299 306 -.623
20 205 341 0 90 148 136 52 206 228 90 75 213 0 67 139 138 52 230 150 380 125 355 .56 50 0 -.458 -.714 .457 .42 100 91 75 33 2.289 1.373 .437 .366 1.984 .728 .61 .475 296 280 104 12 4600 8370 30 35 313 318 -.458

Total number of rows: 43008

Table truncated, full table size 9041 Kbytes.




Supplementary data files not provided
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