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Sample GSM6271 Query DataSets for GSM6271
Status Public on Apr 15, 2004
Title AML 74
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 74
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=650650LaserPower=3.994.64
Lot batch = shcz080
 
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
1 393 624 0 273 242 231 72 420 1321 1125 1168 1364 0 487 201 196 63 204 1172 1376 1217 1421 .83 90 0 1.48 1.63 3.073 2.833 88 86 100 100 .373 .358 2.679 2.972 1.952 2.79 3.096 2.764 1545 1561 355 52 2210 7830 22 31 28 37 1.48
2 5034 5297 0 3279 283 263 105 5105 747 530 517 734 0 314 223 217 67 226 552 778 539 765 .88 90 0 -3.209 -3.225 .112 .104 100 100 98 88 9.632 9.247 .104 .103 2.13 .108 .107 .091 5635 5551 283 52 2350 7840 23 32 42 51 -3.209
3 2250 2479 0 1543 240 229 77 2403 1605 1405 1301 1501 0 732 205 200 53 208 1464 1672 1355 1564 .96 80 0 -.715 -.731 .671 .571 100 100 100 100 1.71 1.642 .585 .578 1.612 .609 .602 .528 3808 3551 262 52 2500 7840 24 32 58 66 -.715
4 898 1113 0 453 232 215 75 853 468 288 274 454 0 101 183 180 52 188 300 488 285 473 .79 80 0 -1.508 -1.654 .396 .317 100 90 100 96 2.962 2.843 .338 .305 2.319 .352 .318 .248 1141 1172 267 52 2640 7840 24 32 72 80 -1.508
5 524 710 0 290 196 186 63 540 554 397 387 544 0 172 165 157 53 164 414 577 403 567 .82 90 0 -.385 -.378 .756 .663 90 88 98 98 1.36 1.306 .735 .739 2.282 .766 .769 .64 937 911 305 52 2790 7830 22 31 86 95 -.385
6 417 585 0 291 176 168 47 443 409 263 244 390 0 158 151 146 43 152 274 426 254 406 .73 80 0 -.693 -.714 .57 .536 96 96 94 84 1.684 1.617 .594 .585 2.352 .618 .61 .496 706 661 244 52 2940 7840 24 32 102 110 -.693
7 620 795 0 370 192 175 116 613 2065 1900 1739 1904 0 979 173 165 60 172 1979 2151 1811 1983 .89 90 0 1.691 1.547 3.55 3.067 94 76 100 100 .323 .31 3.1 2.805 1.954 3.229 2.922 3.02 2513 2359 323 52 3090 7840 23 32 116 125 1.691
8 428 592 0 225 207 164 191 380 328 167 147 308 0 76 180 161 82 168 174 342 153 321 .64 90 0 -1.127 -1.483 .456 .376 75 57 86 46 2.275 2.184 .439 .343 2.379 .458 .358 .247 547 575 339 52 3230 7850 24 33 130 139 -1.127
9 116 266 0 77 153 150 36 132 421 286 288 423 0 86 142 135 41 141 298 439 300 441 .7 90 0 1.174 1.371 2.5 2.218 90 76 100 100 .462 .443 2.167 2.483 2.143 2.257 2.586 2.209 418 404 301 52 3380 7850 24 33 145 154 1.174
10 379 529 0 229 154 150 43 403 256 121 112 247 0 89 140 135 43 141 126 267 117 257 .46 90 0 -1.677 -1.7 .303 .289 94 88 78 59 3.331 3.197 .3 .296 3.554 .313 .308 .213 524 491 288 52 3520 7850 24 33 159 168 -1.677
11 664 819 0 497 160 155 46 688 324 187 170 307 0 150 145 137 47 143 195 338 177 320 .41 80 0 -1.82 -1.907 .267 .227 96 90 82 73 3.679 3.532 .272 .256 3.684 .283 .267 .14 875 834 276 52 3670 7840 24 32 175 183 -1.82
12 1589 1749 0 941 165 160 50 1681 1368 1227 1067 1208 0 562 153 141 63 147 1278 1425 1111 1258 .92 70 0 -.395 -.516 .799 .687 100 96 100 100 1.37 1.315 .73 .671 1.603 .76 .699 .701 2908 2656 213 32 3820 7840 24 31 190 197 -.395
13 519 678 0 377 159 159 36 551 965 819 800 946 0 438 148 146 43 152 853 1005 833 985 .88 80 0 .631 .683 1.732 1.608 94 88 100 100 .673 .646 1.486 1.541 1.928 1.548 1.606 1.329 1370 1319 261 52 3960 7850 25 33 204 212 .631
14 90 254 0 110 163 164 37 111 352 202 143 293 0 185 156 150 43 156 210 367 149 305 .74 90 0 .923 .727 1.693 1.608 78 59 88 78 .55 .528 1.82 1.589 2.385 1.896 1.655 1.872 313 233 322 52 4110 7840 23 32 218 227 .923
15 535 700 0 266 167 165 39 516 7732 7585 8270 8417 0 3943 170 147 177 153 7901 8054 8615 8768 .92 90 0 3.937 4.009 14.254 14.415 94 92 100 100 .068 .065 14.7 15.458 1.593 15.312 16.102 15.765 8101 8805 317 52 4250 7840 23 32 232 241 3.937
16 2649 2808 0 2479 163 159 38 2909 4789 4644 4057 4202 0 3132 164 145 161 151 4838 4989 4226 4377 .95 100 0 .734 .674 2.151 1.589 95 92 100 97 .626 .601 1.596 1.532 2.371 1.663 1.595 1.46 7553 6706 392 80 4410 7850 24 34 248 258 .734
17 667 825 0 691 161 158 38 764 3037 2892 2833 2978 0 1970 150 145 40 151 3013 3164 2951 3102 .92 100 0 1.979 2.145 4.924 4.096 86 80 100 100 .264 .254 3.785 4.247 2.175 3.943 4.424 3.453 3656 3500 325 80 4560 7850 24 34 263 273 1.979
18 134 292 0 98 194 158 433 145 217 69 38 186 0 95 161 148 99 154 72 226 40 194 .23 90 0 -1.012 -1.759 .344 .284 0 0 26 9 2.101 2.017 .476 .284 4.045 .496 .295 .44 214 172 296 52 4690 7840 23 32 276 285 -1.012
19 555 716 0 308 166 161 39 529 407 262 244 389 0 109 152 145 57 151 273 424 254 405 .74 60 0 -.955 -1.127 .592 .51 93 90 96 93 2.019 1.938 .495 .44 2.334 .516 .458 .365 791 799 158 32 4850 7850 26 32 294 300 -.955
20 366 524 0 315 163 158 39 408 573 435 404 542 0 234 142 138 37 144 453 597 421 565 .86 90 0 .151 .201 1.236 1.053 88 82 100 100 .938 .9 1.066 1.104 2.012 1.111 1.15 .921 843 770 303 52 4990 7850 24 33 306 315 .151

Total number of rows: 43008

Table truncated, full table size 9151 Kbytes.




Supplementary data files not provided

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