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Sample GSM6276 Query DataSets for GSM6276
Status Public on Apr 15, 2004
Title AML 10
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 10
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=690640LaserPower=3.994.63
Lot batch = shcz084
 
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
1 732 834 0 410 120 102 223 655 545 431 421 535 0 313 124 114 113 211 798 1009 780 991 .91 90 0 .285 .091 .689 .689 76 61 76 63 1.52 .821 .658 .575 2.997 1.219 1.065 .555 1086 1153 356 52 2020 7670 30 39 25 34 .285
2 1300 1407 0 929 125 107 262 1273 1617 1501 1564 1680 0 1009 129 116 127 215 2780 2994 2896 3111 .98 80 0 1.127 1.156 1.233 1.223 78 67 100 84 .848 .458 1.179 1.203 1.382 2.184 2.228 1.141 2774 2864 254 52 2170 7670 31 39 41 49 1.127
3 1672 1778 0 1436 112 106 49 1880 1786 1677 1304 1413 0 1280 113 109 38 202 3106 3307 2415 2617 .97 90 0 .724 .53 .944 .875 100 96 100 100 1.121 .605 .892 .78 1.687 1.652 1.444 .888 3557 2976 317 52 2310 7680 31 40 54 63 .724
4 611 716 0 414 111 105 52 681 326 219 192 299 0 170 110 107 38 198 406 604 356 554 .87 80 0 -.748 -.781 .285 .321 100 98 82 75 3.11 1.679 .322 .314 1.909 .596 .582 .315 900 803 255 52 2460 7680 32 40 70 78 -.748
5 699 803 0 419 111 104 47 669 422 308 245 359 0 269 120 114 46 211 570 781 454 665 .91 80 0 -.23 -.624 .387 .423 96 90 88 75 2.172 1.173 .46 .351 1.706 .853 .649 .506 977 944 261 52 2590 7670 31 39 83 91 -.23
6 731 841 0 377 117 110 51 723 454 340 302 416 0 206 118 114 40 211 630 841 559 770 .93 70 0 -.199 -.386 .432 .434 96 96 93 90 2.126 1.148 .47 .413 1.634 .871 .765 .48 1063 1033 218 32 2750 7670 31 38 99 106 -.199
7 201 302 0 583 106 101 32 544 1275 1164 419 530 0 1305 114 111 38 206 2156 2361 776 981 .96 100 0 1.986 1.949 1.871 2.041 90 83 96 93 .467 .252 2.14 2.085 1.722 3.962 3.86 2.255 1708 620 380 80 2900 7680 31 41 113 123 1.986
8 798 902 0 416 108 104 28 701 246 135 114 225 0 103 114 111 38 206 250 456 211 417 .81 90 0 -1.487 -1.918 .223 .197 96 94 80 69 5.193 2.804 .193 .143 2.223 .357 .265 .196 836 912 300 52 3040 7670 30 39 127 136 -1.487
9 864 968 0 276 124 104 264 802 504 396 377 485 0 203 112 108 36 200 733 933 698 898 .69 90 0 -.129 -.307 .464 .489 90 82 100 96 2.025 1.094 .494 .436 1.497 .914 .808 .315 1198 1241 288 52 3190 7680 31 40 142 151 -.129
10 860 965 0 366 124 105 260 824 301 193 198 306 0 87 113 108 38 200 357 557 367 567 .82 90 0 -1.205 -1.23 .247 .246 88 78 94 88 4.269 2.305 .234 .23 1.932 .434 .426 .206 1017 1058 298 52 3330 7680 31 40 156 165 -1.205
11 710 816 0 1110 109 106 31 1189 400 290 189 299 0 296 115 110 39 204 537 741 350 554 .94 80 0 -1.147 -1.02 .241 .251 100 98 75 73 4.1 2.214 .244 .266 2.397 .452 .493 .245 1479 899 275 52 3490 7680 32 40 173 181 -1.147
12 1652 1759 0 1349 110 107 31 1962 2216 2105 1797 1908 0 1340 118 111 48 206 3898 4104 3328 3533 .97 80 0 .99 1.01 1.183 1.092 100 100 100 100 .932 .503 1.073 1.088 1.48 1.987 2.014 1.04 4067 3449 254 52 3630 7680 32 40 187 195 .99
13 295 401 0 461 108 106 26 502 726 619 360 467 0 589 114 107 41 198 1146 1344 667 865 .92 80 0 1.191 1.176 1.208 1.251 96 90 96 92 .811 .438 1.233 1.22 2.082 2.283 2.26 1.279 1121 655 244 52 3780 7690 33 41 202 210 1.191
14 491 593 0 238 106 102 26 483 347 247 243 343 0 161 104 100 32 185 457 643 450 635 .89 70 0 -.079 -.126 .434 .504 100 100 93 84 1.955 1.056 .511 .495 1.732 .947 .916 .532 730 734 200 32 3920 7680 32 39 216 223 -.079
15 1068 1175 0 437 109 107 26 968 12571 12463 11338 11446 0 7609 117 108 67 200 23080 23280 20996 21196 .93 90 0 4.575 4.297 12.334 12.271 98 98 100 100 .078 .042 12.875 10.616 1.534 23.843 19.659 14.98 13431 12406 328 52 4060 7670 30 39 229 238 4.575
16 4034 4141 0 3189 110 107 29 4152 8670 8561 7710 7819 0 6789 126 109 89 202 15854 16056 14278 14480 .98 90 0 1.933 1.823 2.176 2.039 100 100 100 100 .485 .262 2.062 1.911 1.562 3.818 3.539 2.111 12713 11744 317 52 4210 7670 30 39 244 253 1.933
17 749 857 0 857 110 108 28 1041 4156 4046 3083 3193 0 3131 118 110 65 204 7493 7696 5709 5913 .97 100 0 2.847 2.93 4.287 3.952 97 95 100 100 .257 .139 3.887 4.116 1.7 7.197 7.623 3.884 5087 3832 396 80 4360 7680 31 41 259 269 2.847
18 931 1038 0 455 109 107 23 832 276 161 149 264 0 114 120 115 41 213 298 511 276 489 .79 60 0 -1.481 -1.755 .199 .204 93 93 87 75 5.168 2.791 .194 .16 2.751 .358 .296 .17 993 1080 160 32 4500 7680 33 39 275 281 -1.481
19 771 878 0 864 108 107 25 954 528 423 229 334 0 404 110 105 35 194 783 978 424 619 .94 90 0 -.284 -.862 .452 .427 98 98 98 88 2.255 1.218 .443 .297 2.017 .821 .55 .435 1377 1000 310 52 4660 7680 31 40 289 298 -.284
20 1233 1342 0 1120 111 109 26 1442 1301 1194 1092 1199 0 880 112 107 37 198 2211 2409 2022 2220 .96 90 0 .617 .714 .966 .892 98 96 100 100 1.208 .652 .828 .886 1.764 1.533 1.64 .792 2636 2325 290 52 4800 7670 30 39 303 312 .617

Total number of rows: 43008

Table truncated, full table size 9532 Kbytes.




Supplementary data files not provided
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