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Sample GSM6346 Query DataSets for GSM6346
Status Public on Apr 15, 2004
Title AML 106
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 106
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix Pro
Software version: 3.0.6.81
Scanning parameters: PMTVolts=690650LaserPower=3.574.68
Lot batch = shdj113
 
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 GPL319
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
1 678 908 0 279 235 230 70 694 350 132 102 320 0 111 217 218 64 316 191 507 148 464 .67 60 0 -1.859 -2.197 .153 .187 100 96 68 43 5.258 3.628 .19 .15 2.2 .276 .218 .217 826 780 159 32 1800 8620 39 45 29 35 -1.859
2 2578 2796 0 947 225 218 61 2697 637 430 406 613 0 182 214 207 67 300 623 923 588 888 .91 80 0 -2.114 -2.131 .153 .158 100 100 100 94 6.272 4.328 .159 .157 1.432 .231 .228 .15 3127 2984 286 52 1950 8630 39 47 43 51 -2.114
3 2548 2769 0 1693 229 221 61 2819 1741 1518 1581 1804 0 933 225 223 66 323 2200 2523 2291 2614 .98 70 0 -.358 -.153 .476 .51 100 100 93 93 1.857 1.281 .538 .62 1.769 .78 .899 .534 4337 4129 219 32 2100 8620 38 45 58 65 -.358
4 474 687 0 346 224 213 56 533 478 279 262 461 0 186 209 199 66 288 404 693 380 668 .74 70 0 -.399 -.32 .517 .474 96 87 81 68 1.91 1.318 .523 .553 1.878 .759 .801 .486 812 736 196 32 2250 8630 39 46 73 80 -.399
5 2361 2563 0 1147 210 202 52 2447 1556 1354 1283 1485 0 700 216 202 87 293 1962 2255 1859 2152 .96 80 0 -.318 -.345 .526 .551 100 100 98 98 1.807 1.247 .553 .543 1.423 .802 .788 .561 3801 3644 268 52 2380 8630 39 47 86 94 -.318
6 625 813 0 212 197 188 46 646 263 73 62 252 0 94 197 190 66 275 106 381 90 365 .39 60 0 -2.61 -2.798 .151 .161 100 100 46 28 8.849 6.106 .113 .099 2.021 .164 .144 .111 719 687 171 32 2530 8630 40 46 102 108 -2.61
7 2318 2511 0 1499 200 193 53 2362 1640 1470 1626 1796 0 909 176 170 58 246 2130 2377 2357 2603 .97 80 0 -.149 .024 .622 .637 100 98 100 98 1.607 1.109 .622 .701 1.399 .902 1.017 .609 3832 3944 274 52 2680 8630 39 47 116 124 -.149
8 1452 1642 0 648 198 190 51 1503 284 106 94 272 0 114 185 178 61 258 154 412 136 394 .67 80 0 -3.29 -3.414 .061 .078 100 100 59 38 14.179 9.784 .071 .065 2.165 .102 .094 .084 1609 1546 254 52 2820 8630 39 47 130 138 -3.29
9 1184 1383 0 342 209 199 58 1200 1178 968 998 1208 0 299 219 210 73 304 1403 1707 1446 1751 .95 90 0 .225 .289 .8 .808 100 100 100 100 1.24 .855 .807 .843 1.293 1.169 1.222 .817 2168 2182 338 52 2970 8620 37 46 144 153 .225
10 767 1006 0 245 286 239 144 752 310 93 91 308 0 119 218 217 73 314 135 449 132 446 .65 50 0 -2.48 -2.54 .144 .152 100 100 50 33 8.086 5.579 .124 .119 1.592 .179 .172 .17 845 858 90 12 3120 8610 38 43 161 166 -2.48
11 11286 11495 0 5386 223 209 82 11492 873 652 518 739 0 461 226 221 72 320 945 1265 751 1071 .9 100 0 -3.604 -3.91 .05 .054 100 100 97 91 17.626 12.162 .057 .046 1.642 .082 .067 .058 12144 11804 392 80 3260 8630 38 48 173 183 -3.604
12 19676 19889 0 9389 220 213 58 18472 11669 11451 12235 12453 0 6289 228 218 76 316 16596 16912 17732 18048 .99 100 0 -.155 -.15 .604 .632 100 100 100 100 1.613 1.113 .62 .622 1.242 .898 .901 .629 29923 31911 358 80 3410 8630 38 48 188 198 -.155
13 1805 2024 0 569 227 219 66 1751 1712 1502 1499 1709 0 611 219 210 71 304 2177 2481 2172 2477 .96 90 0 .314 .267 .824 .877 100 100 100 100 1.166 .804 .858 .83 1.344 1.243 1.204 .887 3253 3304 259 52 3550 8630 38 47 202 211 .314
14 891 1110 0 360 231 219 64 846 802 594 604 812 0 276 217 208 69 301 861 1162 875 1177 .94 120 0 .025 -.026 .686 .685 99 97 95 93 1.424 .983 .702 .678 1.36 1.018 .982 .726 1440 1495 454 120 3700 8630 37 49 216 228 .025
15 3420 3632 0 1059 220 212 52 3389 6905 6704 7075 7276 0 1978 210 201 67 291 9716 10007 10254 10545 .99 100 0 1.519 1.584 1.995 2.005 100 100 100 100 .506 .349 1.978 2.069 1.132 2.867 2.998 1.974 10093 10495 306 80 3850 8630 38 48 232 242 1.519
16 20442 20661 0 5382 224 219 55 20989 33023 32819 31465 31669 0 9492 214 204 74 296 47564 47859 45601 45897 .99 110 0 1.18 1.158 1.55 1.582 100 100 100 100 .64 .441 1.564 1.539 1.138 2.266 2.231 1.581 53808 51907 394 80 3990 8630 37 48 245 256 1.18
17 3744 3964 0 613 233 220 118 3721 3779 3555 3633 3857 0 863 246 224 151 325 5152 5477 5265 5590 .99 110 0 .469 .492 .936 .97 100 100 100 100 1.047 .722 .955 .97 1.17 1.385 1.406 .988 7276 7377 403 80 4140 8620 36 47 260 271 .469
18 61 283 0 322 234 222 126 170 296 60 19 255 0 145 257 236 158 342 87 429 28 370 .55 100 -50 -1.147 .58 .524 32 15 17 5 2.833 1.955 .353 .311 3.851 .512 .451 .371 230 80 333 80 4290 8630 38 48 276 286 -.967
19 7365 7580 0 2098 224 215 58 7301 8352 8135 8698 8915 0 2338 230 217 81 314 11790 12104 12606 12920 .99 100 0 .691 .775 1.107 1.11 100 100 100 100 .897 .619 1.114 1.181 1.149 1.615 1.712 1.116 15436 16063 313 80 4440 8630 38 48 291 301 .691
20 4324 4540 0 849 225 216 61 4419 4456 4260 4333 4529 0 803 210 196 75 284 6174 6458 6280 6564 .99 110 0 .482 .538 .964 .968 100 100 100 100 1.037 .716 .964 1.002 1.151 1.397 1.452 .965 8679 8657 366 80 4580 8630 37 48 304 315 .482

Total number of rows: 43008

Table truncated, full table size 9108 Kbytes.




Supplementary data files not provided
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