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Sample GSM6245 Query DataSets for GSM6245
Status Public on Apr 15, 2004
Title AML 100
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 100
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=680640LaserPower=3.413.81
Lot batch = shco044
 
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 GPL317
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
1 161 294 0 70 134 133 32 182 244 120 134 258 0 57 126 124 38 155 150 305 168 323 .69 60 0 -.279 .057 .584 .642 100 100 87 71 1.517 1.213 .659 .832 2.098 .824 1.04 .641 302 295 176 32 2150 7770 70 76 52 58 -.279
2 198 340 0 71 141 142 30 210 224 100 105 229 0 51 129 124 37 155 125 280 131 286 .58 70 0 -.748 -.593 .443 .503 100 100 87 71 2.1 1.68 .476 .53 2.339 .595 .663 .469 310 303 233 32 2300 7770 69 76 66 73 -.748
3 1362 1493 0 473 133 131 32 1321 259 133 127 253 0 73 127 126 38 158 166 324 159 316 .72 100 0 -2.99 -3.101 .102 .103 98 97 92 77 9.932 7.946 .101 .093 2.121 .126 .117 .087 1454 1489 424 80 2470 7770 68 78 82 92 -2.99
4 2042 2173 0 1288 134 131 30 2125 2566 2439 2042 2169 0 1599 129 127 37 159 3049 3208 2553 2711 .95 80 0 .521 .322 1.242 1.199 100 98 100 100 .871 .697 1.148 1 1.941 1.435 1.25 1.184 4564 4084 254 52 2600 7770 69 77 96 104 .521
5 414 550 0 270 151 136 112 425 544 414 401 531 0 219 136 130 45 163 518 680 501 664 .89 60 0 .284 .276 .999 .963 90 68 96 93 1.027 .821 .974 .969 2.025 1.218 1.211 .9 839 815 158 32 2740 7770 70 76 111 117 .284
6 81 225 0 58 154 144 92 79 231 95 90 226 0 62 141 136 43 170 119 289 113 283 .48 80 0 .588 .474 1.038 .952 40 3 78 53 .832 .665 1.203 1.111 2.94 1.503 1.389 1.415 174 171 244 52 2890 7780 70 78 125 133 .588
7 123 264 0 66 144 141 32 120 4592 4455 4492 4629 0 1693 145 137 55 171 5569 5740 5615 5786 .76 80 0 5.536 5.513 32.24 32.604 86 80 100 100 .027 .022 37.125 36.52 1.646 46.406 45.65 42.392 4575 4615 266 52 3040 7770 69 77 140 148 5.536
8 2849 2994 0 1519 158 145 67 2609 3207 3063 3333 3477 0 1672 151 144 54 180 3829 4009 4166 4346 .95 80 0 .553 .548 1.337 1.168 98 94 100 100 .852 .681 1.174 1.17 2.29 1.468 1.462 1.162 5672 6182 230 52 3180 7770 69 77 154 162 .553
9 420 566 0 229 155 146 65 446 3929 3793 3230 3366 0 2153 140 136 43 170 4741 4911 4038 4208 .9 80 0 3.41 3.265 8.348 8.357 100 94 100 100 .118 .094 8.504 7.69 1.665 10.631 9.613 9.481 4239 3650 246 52 3330 7770 69 77 169 177 3.41
10 33 166 0 88 135 133 30 68 166 37 22 151 0 72 132 129 39 161 46 208 28 189 .54 100 -50 -.263 .871 .75 52 40 37 22 1.838 1.47 .544 .667 3.66 .68 .833 .804 105 55 397 80 3460 7750 66 76 181 191 -.556
11 1254 1391 0 400 138 137 28 1263 567 442 446 571 0 135 128 125 37 156 553 709 558 714 .9 100 0 -1.193 -1.169 .355 .343 100 100 100 100 2.857 2.286 .35 .356 1.523 .437 .445 .316 1705 1700 398 80 3640 7770 68 78 199 209 -1.193
12 365 501 0 188 138 136 30 365 352 223 191 320 0 120 129 129 37 161 279 440 239 400 .83 60 0 -.389 -.612 .578 .576 100 100 96 90 1.637 1.309 .611 .523 1.972 .764 .654 .582 588 556 164 32 3780 7760 69 75 215 221 -.389
13 364 498 0 161 136 134 27 362 342 214 213 341 0 86 132 128 40 160 268 428 266 426 .81 70 0 -.436 -.451 .589 .601 100 100 100 90 1.692 1.353 .591 .585 1.624 .739 .731 .549 576 577 216 32 3920 7760 68 75 228 235 -.436
14 130 267 0 63 138 137 29 130 210 83 81 208 0 60 128 127 39 159 104 263 101 260 .3 50 0 -.325 -.361 .548 .682 91 83 75 50 1.566 1.253 .638 .623 3.803 .798 .779 .521 213 211 104 12 4050 7760 69 74 242 247 -.325
15 2250 2379 0 978 132 129 32 2258 1435 1314 1270 1391 0 535 126 121 35 151 1643 1794 1588 1739 .93 80 0 -.459 -.503 .614 .594 100 100 100 100 1.718 1.375 .582 .564 1.649 .727 .706 .543 3572 3520 288 52 4210 7770 69 77 257 265 -.459
16 674 808 0 264 136 134 31 676 411 287 263 387 0 134 128 124 36 155 359 514 329 484 .86 90 0 -.914 -1.036 .417 .446 100 100 94 94 2.355 1.884 .425 .39 1.56 .531 .488 .417 963 937 346 52 4350 7760 67 76 270 279 -.914
17 164 303 0 84 141 139 30 173 205 80 83 208 0 45 127 125 36 156 100 256 104 260 .48 70 0 -.791 -.661 .432 .397 100 93 78 56 2.163 1.73 .462 .506 2.726 .578 .633 .41 253 247 223 32 4510 7760 68 75 287 294 -.791
18 95 226 0 47 133 131 28 98 201 83 84 202 0 54 119 118 34 148 104 251 105 253 .47 60 0 .082 .144 .793 .852 93 78 78 62 1.181 .945 .847 .884 2.885 1.059 1.105 1.067 181 179 168 32 4640 7770 70 76 301 307 .082
19 578 703 0 154 129 125 28 587 405 289 301 417 0 108 120 116 37 145 361 506 376 521 .83 100 0 -.7 -.619 .457 .516 100 100 98 96 2.031 1.625 .492 .521 1.851 .615 .651 .456 876 879 400 80 4800 7760 67 77 315 325 -.7
20 436 568 0 174 135 132 31 449 476 355 374 495 0 147 127 121 41 151 444 595 468 619 .85 80 0 -.017 .101 .775 .781 100 98 100 96 1.265 1.012 .791 .858 1.897 .988 1.072 .772 804 810 253 52 4930 7760 68 76 329 337 -.017

Total number of rows: 43008

Table truncated, full table size 9149 Kbytes.




Supplementary data files not provided
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