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Sample GSM6291 Query DataSets for GSM6291
Status Public on Apr 15, 2004
Title AML 95
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 95
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=3.994.58
Lot batch = shcz088
 
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
1 603 751 0 154 178 148 261 622 1536 1440 1462 1558 0 397 106 96 58 200 3000 3200 3046 3246 .63 90 0 2.27 2.337 2.281 2.309 100 73 100 100 .432 .207 2.315 2.425 1.428 4.823 5.051 1.878 2062 2065 348 52 2010 7490 28 37 16 25 2.27
2 4398 4545 0 1973 153 147 48 4848 16015 15913 14816 14918 0 7408 110 102 54 213 33152 33365 30867 31079 .95 90 0 2.774 2.811 3.171 3.154 100 100 100 100 .305 .146 3.282 3.369 1.391 6.838 7.018 3.524 20761 19214 289 52 2160 7500 29 38 31 40 2.774
3 3884 4035 0 3003 156 151 46 4550 1905 1805 1903 2003 0 980 105 100 40 208 3760 3969 3965 4173 .94 90 0 -.275 .03 .385 .402 100 100 100 100 2.521 1.21 .397 .49 1.481 .826 1.021 .361 6355 5787 326 52 2300 7490 28 37 45 54 -.275
4 812 955 0 410 147 143 31 766 254 158 146 242 0 107 101 96 35 200 329 529 304 504 .84 80 0 -1.219 -1.417 .184 .19 100 100 88 67 4.848 2.327 .206 .18 1.948 .43 .375 .203 924 958 264 52 2450 7500 30 38 61 69 -1.219
5 487 633 0 547 151 146 33 714 510 413 296 393 0 376 101 97 34 202 860 1063 617 819 .94 100 0 .269 .341 .517 .544 100 98 92 82 1.729 .83 .578 .608 1.9 1.205 1.266 .615 1127 783 364 80 2600 7500 29 39 75 85 .269
6 1160 1317 0 307 159 157 40 1141 536 439 434 531 0 191 102 97 36 202 915 1117 904 1106 .92 70 0 -.319 -.359 .355 .353 100 100 100 96 2.599 1.248 .385 .374 1.464 .802 .779 .378 1580 1594 205 32 2740 7490 29 36 90 97 -.319
7 1003 1148 0 753 147 145 36 1133 2613 2519 2335 2429 0 1622 99 94 32 196 5248 5444 4865 5060 .96 90 0 2.212 2.278 2.321 2.342 100 100 100 100 .45 .216 2.223 2.328 1.36 4.632 4.85 2.253 3652 3338 335 52 2890 7500 29 38 104 113 2.212
8 896 1045 0 211 153 149 38 897 346 253 257 350 0 109 104 93 40 194 527 721 535 729 .87 70 0 -.767 -.743 .263 .291 100 100 100 100 3.545 1.702 .282 .287 1.492 .588 .598 .277 1150 1153 219 32 3030 7500 30 37 119 126 -.767
9 806 955 0 333 152 149 49 747 354 259 231 326 0 120 102 95 53 198 540 738 481 679 .81 70 0 -.469 -.744 .358 .349 100 100 100 93 2.884 1.384 .347 .287 1.823 .722 .597 .296 1006 1037 204 32 3180 7500 30 37 134 141 -.469
10 778 915 0 199 140 137 37 746 179 86 81 174 0 55 98 93 33 194 179 373 169 363 .67 90 0 -2.058 -2.205 .104 .108 100 100 86 59 8.674 4.164 .115 .104 1.904 .24 .217 .107 832 859 328 52 3320 7500 29 38 147 156 -2.058
11 4099 4240 0 1208 146 141 39 3846 490 398 374 466 0 159 98 92 33 192 829 1021 779 971 .92 70 0 -2.214 -2.395 .101 .106 100 100 100 100 9.663 4.638 .103 .091 1.435 .216 .19 .097 4244 4473 218 32 3470 7500 30 37 163 170 -2.214
12 3518 3664 0 2192 151 146 45 3782 3087 2993 3073 3167 0 1738 99 94 39 196 6235 6431 6402 6598 .94 70 0 .721 .864 .772 .737 100 100 100 100 1.264 .607 .791 .874 1.465 1.649 1.82 .782 6775 6591 220 32 3620 7490 29 36 178 185 .721
13 1302 1440 0 694 139 138 33 1399 1893 1802 1669 1760 0 1277 96 91 38 190 3754 3944 3477 3667 .94 70 0 1.424 1.417 1.095 1.155 100 100 100 100 .776 .373 1.288 1.282 1.718 2.683 2.671 1.53 3201 2971 207 32 3760 7490 29 36 192 199 1.424
14 239 379 0 190 148 140 79 285 176 84 87 179 0 69 101 92 41 192 175 367 181 373 .54 80 0 -.704 -.399 .325 .334 80 71 67 53 3.393 1.629 .295 .364 3.143 .614 .758 .205 369 326 265 52 3910 7500 30 38 207 215 -.704
15 1015 1152 0 180 138 137 28 994 15998 15901 15953 16050 0 3435 105 97 49 202 33127 33329 33235 33438 .97 90 0 5.059 5.033 15.921 16.048 100 100 100 100 .063 .03 15.997 15.717 1.175 33.327 32.744 16.481 16895 16968 313 52 4050 7490 28 37 220 229 5.059
16 8458 8595 0 2345 144 137 56 7371 10293 10197 11153 11249 0 4184 103 96 50 200 21244 21444 23235 23435 .97 90 0 1.527 1.458 1.306 1.344 100 100 100 100 .723 .347 1.383 1.319 1.334 2.882 2.747 1.453 17568 19611 317 52 4200 7490 28 37 235 244 1.527
17 1506 1642 0 780 147 136 66 1446 7595 7498 7762 7859 0 3392 100 97 35 202 15621 15823 16171 16373 .96 100 0 3.433 3.425 5.765 5.265 98 95 100 100 .193 .093 5.185 5.154 1.567 10.803 10.738 5.105 8944 9268 377 80 4350 7500 29 39 250 260 3.433
18 606 767 0 147 171 161 62 587 162 67 73 168 0 53 97 95 33 198 140 338 152 350 .47 50 0 -2.072 -1.994 .094 .137 100 100 75 58 8.761 4.205 .114 .12 2.645 .238 .251 .088 654 679 98 12 4490 7480 29 34 266 271 -2.072
19 1416 1553 0 1463 153 137 79 1875 648 559 514 603 0 419 93 89 32 185 1165 1350 1071 1256 .93 80 0 -.687 -.403 .313 .284 100 96 96 92 3.354 1.61 .298 .363 2.026 .621 .756 .274 2434 1930 264 52 4640 7490 29 37 280 288 -.687
20 1675 1806 0 1029 138 131 40 1728 886 794 706 798 0 578 95 92 34 192 1654 1846 1471 1663 .94 80 0 -.063 -.188 .397 .417 100 100 94 90 2.176 1.045 .459 .421 1.731 .957 .878 .48 2522 2381 236 52 4780 7490 29 37 294 302 -.063

Total number of rows: 43008

Table truncated, full table size 9618 Kbytes.




Supplementary data files not provided
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