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Sample GSM6295 Query DataSets for GSM6295
Status Public on Apr 15, 2004
Title AML 47
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 47
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=740640LaserPower=4.034.17
Lot batch = shcz094
 
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
1 576 763 0 175 191 187 49 578 695 417 474 752 0 208 279 278 102 343 515 858 585 928 .84 70 0 -.167 .023 .701 .747 100 100 90 81 1.386 1.123 .721 .823 1.642 .891 1.016 .892 995 1050 220 32 2050 7670 23 30 45 52 -.167
2 3806 3990 0 2171 204 184 81 3442 1007 744 788 1051 0 597 271 263 98 325 919 1243 973 1298 .94 80 0 -1.906 -1.968 .191 .223 100 98 80 73 4.626 3.747 .216 .207 1.791 .267 .256 .231 4186 4594 274 52 2200 7660 22 30 60 68 -1.906
3 2606 2789 0 1259 202 183 80 2416 2064 1804 1985 2245 0 1011 270 260 86 321 2227 2548 2451 2772 .96 80 0 -.117 -.089 .774 .762 92 92 96 90 1.339 1.085 .747 .762 1.703 .922 .94 .757 4220 4591 268 52 2350 7670 23 31 75 83 -.117
4 548 725 0 394 182 177 41 568 3434 3175 3419 3678 0 1875 275 259 102 320 3920 4240 4221 4541 .96 90 0 2.787 2.945 5.765 5.329 90 86 94 94 .179 .145 5.59 6.239 1.46 6.901 7.703 5.454 3743 3967 328 52 2490 7670 22 31 88 97 2.787
5 994 1183 0 413 224 189 99 1021 883 603 608 888 0 306 284 280 89 346 744 1090 751 1096 .9 70 0 -.456 -.405 .605 .62 96 93 96 93 1.693 1.371 .591 .612 1.726 .729 .755 .63 1624 1602 212 32 2640 7670 23 30 104 111 -.456
6 1030 1217 0 350 199 187 62 921 1191 927 1005 1269 0 371 275 264 92 326 1144 1470 1241 1567 .94 70 0 .313 .269 .958 1.004 96 93 93 93 .994 .805 1.007 .976 1.493 1.243 1.205 1.014 1848 2035 218 32 2790 7670 23 30 119 126 .313
7 1043 1217 0 817 176 174 40 1140 2198 1949 1670 1919 0 1374 262 249 92 307 2406 2714 2062 2369 .98 90 0 1.078 .983 1.878 1.785 94 90 96 96 .585 .474 1.71 1.601 1.852 2.111 1.977 1.715 3089 2713 309 52 2930 7670 22 31 132 141 1.078
8 759 931 0 328 180 172 47 702 391 156 173 408 0 127 242 235 85 290 193 483 214 504 .64 80 0 -1.866 -1.829 .23 .256 96 96 80 50 4.5 3.645 .222 .228 2.321 .274 .281 .232 858 932 277 52 3070 7680 24 32 147 155 -1.866
9 612 786 0 284 180 174 45 581 615 382 403 636 0 259 238 233 80 288 472 759 498 785 .87 60 0 -.301 -.299 .671 .64 96 96 90 78 1.521 1.232 .657 .658 1.63 .812 .813 .734 963 1015 165 32 3220 7670 24 30 163 169 -.301
10 675 847 0 297 182 172 52 594 341 93 92 340 0 128 255 248 82 306 115 421 114 420 .6 80 0 -2.371 -2.571 .21 .22 94 92 53 32 6.387 5.174 .157 .136 2.45 .193 .168 .229 687 767 277 52 3360 7680 24 32 176 184 -2.371
11 3526 3706 0 1429 187 180 51 3038 1216 961 972 1227 0 595 264 255 112 315 1186 1501 1200 1515 .96 60 0 -1.357 -1.555 .313 .311 96 93 87 87 3.161 2.561 .316 .276 2.186 .391 .34 .341 3999 4498 172 32 3510 7680 25 31 192 198 -1.357
12 3750 3926 0 2094 194 176 75 3452 2572 2328 2036 2280 0 1531 264 244 94 301 2874 3175 2514 2815 .97 70 0 -.264 -.577 .656 .697 100 100 100 100 1.483 1.201 .674 .543 1.36 .833 .67 .678 5780 5786 220 32 3650 7670 23 30 205 212 -.264
13 1011 1181 0 464 173 170 38 951 991 757 714 948 0 437 236 234 78 289 935 1223 881 1170 .91 60 0 -.025 -.198 .836 .746 96 93 96 96 1.256 1.018 .796 .706 2.188 .983 .872 .837 1708 1725 170 32 3810 7670 24 30 222 228 -.025
14 435 606 0 101 172 171 39 423 575 348 323 550 0 192 233 227 88 280 430 710 399 679 .78 50 0 .022 -.125 .724 .711 100 100 100 75 1.216 .985 .823 .743 1.545 1.016 .917 1.104 771 758 104 12 3940 7680 25 30 235 240 .022
15 544 711 0 257 169 167 38 467 4531 4309 5167 5389 0 1928 231 222 77 274 5320 5594 6379 6653 .95 90 0 3.51 3.552 9.357 9.085 90 88 100 100 .108 .088 9.227 9.498 1.307 11.391 11.726 8.946 4776 5711 348 52 4090 7670 22 31 248 257 3.51
16 5948 6119 0 2959 174 171 44 5308 10241 10011 11153 11383 0 5252 244 230 88 284 12359 12643 13769 14053 .98 90 0 1.219 1.211 2.371 1.97 94 92 100 100 .53 .429 1.886 1.875 2.206 2.328 2.315 1.861 15319 17101 327 52 4240 7670 22 31 263 272 1.219
17 1150 1314 0 786 169 164 40 1116 5415 5187 5278 5506 0 3127 246 228 97 281 6404 6685 6516 6798 .97 100 0 2.521 2.502 5.202 4.612 86 85 100 100 .215 .174 4.648 4.59 1.74 5.738 5.666 4.489 6303 6428 391 80 4390 7680 23 33 278 288 2.521
18 545 713 0 158 174 168 52 541 342 146 147 343 0 78 216 196 96 242 180 422 181 423 .61 50 0 -1.586 -1.586 .232 .277 100 100 66 25 3.705 3.001 .27 .27 2.223 .333 .333 .302 687 692 93 12 4520 7670 24 29 293 298 -1.586
19 2117 2285 0 1246 174 168 42 2174 1275 1056 991 1210 0 580 228 219 76 270 1304 1574 1223 1494 .95 70 0 -.738 -.791 .514 .498 93 93 93 93 2.059 1.668 .486 .468 1.649 .6 .578 .463 3230 3108 225 32 4670 7670 23 30 307 314 -.738
20 1989 2156 0 928 172 167 39 1888 1205 983 1026 1248 0 512 228 222 73 274 1214 1488 1267 1541 .96 70 0 -.638 -.651 .509 .53 96 96 93 93 1.921 1.556 .521 .516 1.892 .643 .637 .528 2871 3015 218 32 4820 7680 24 31 322 329 -.638

Total number of rows: 43008

Table truncated, full table size 9353 Kbytes.




Supplementary data files not provided
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