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Sample GSM6244 Query DataSets for GSM6244
Status Public on Apr 15, 2004
Title AML 26
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 26
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=660620LaserPower=3.324.45
Lot batch = shco040
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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 �m 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 �m 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 �m 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 7 91 0 23 90 84 51 11 99 8 3 94 0 34 93 91 28 91 8 99 3 94 .14 100 -50 -1.222 1.489 1.645 5 1 18 6 1.375 1.375 .727 .429 5.145 .727 .429 .102 19 10 397 80 1960 7720 71 81 63 73 -.459
2 20 104 0 75 90 84 55 38 103 10 5 98 0 51 97 93 29 93 10 103 5 98 .4 100 -50 -2 .915 .82 21 2 26 5 3.8 3.8 .263 .25 3.556 .263 .25 .258 48 25 339 80 2110 7720 71 81 78 88 -1.926
3 132 218 0 86 89 86 23 146 113 16 11 108 0 39 100 97 33 97 16 113 11 108 .27 100 0 -3.19 -3.585 .197 .212 96 90 25 11 9.125 9.125 .11 .083 3.158 .11 .083 .166 162 143 363 80 2270 7720 71 81 94 104 -3.19
4 306 394 0 284 91 88 22 374 416 320 249 345 0 188 98 96 38 96 320 416 249 345 .87 70 0 -.225 -.297 .931 .903 93 93 100 96 1.169 1.169 .856 .814 1.834 .856 .814 .805 694 555 176 32 2410 7730 73 80 109 116 -.225
5 24 111 0 53 90 87 22 36 141 46 30 125 0 63 100 95 33 95 46 141 30 125 .37 100 -50 .322 1.551 1.247 51 32 43 26 .783 .783 1.278 1.25 2.769 1.278 1.25 2.141 82 54 388 80 2550 7720 71 81 122 132 .354
6 0 91 0 20 95 91 27 0 143 43 30 130 0 67 106 100 35 100 43 143 30 130 .08 60 -100 2.952 3.151 12 0 46 28 2.779 .051 43 30 88 32 2640 7690 70 76 133 139
7 23 111 0 27 89 88 25 26 553 457 447 543 0 192 107 96 49 96 457 553 447 543 .41 90 0 4.136 4.281 16.327 15.69 44 15 100 96 .057 .057 17.577 19.435 2.01 17.577 19.435 16.927 483 470 328 52 2850 7730 72 81 152 161 4.136
8 419 505 0 248 88 86 23 438 915 812 759 862 0 340 114 103 48 103 812 915 759 862 .93 80 0 .891 .857 2.036 1.932 98 96 100 100 .539 .539 1.854 1.811 1.66 1.854 1.811 1.759 1250 1178 232 52 3000 7730 73 81 168 176 .891
9 62 147 0 54 89 85 26 66 658 550 492 600 0 345 119 108 53 108 550 658 492 600 .7 100 0 3.059 2.988 8.518 7.977 76 58 98 95 .12 .12 8.333 7.935 1.964 8.333 7.935 9.948 616 554 307 80 3140 7730 72 82 181 191 3.059
10 6 92 0 25 89 86 24 12 101 2 -4 95 0 32 109 99 46 99 2 101 95 .28 100 -50 1.071 1.072 22 6 8 2 6 6 .167 3.961 .167 3.341 14 2 338 80 3270 7720 71 81 194 204 -2.585
11 163 249 0 86 88 86 22 164 149 52 46 143 0 51 103 97 34 97 52 149 46 143 .46 110 0 -1.657 -1.825 .325 .363 93 92 58 35 3.154 3.154 .317 .282 2.689 .317 .282 .291 216 209 472 80 3430 7730 71 82 209 220 -1.657
12 63 150 0 50 88 87 21 69 148 52 46 142 0 54 101 96 30 96 52 148 46 142 .37 70 -100 -.454 .967 1.01 87 65 62 37 1.327 1.327 .754 .73 2.767 .754 .73 1.191 121 109 216 32 3570 7720 72 79 225 232 -.408
13 49 135 0 903 93 86 26 232 815 721 33 127 0 2864 98 94 32 94 721 815 33 127 .98 60 -100 -.57 1.069 .885 68 46 50 28 .322 .322 3.108 .673 3.45 3.108 .673 3.227 953 82 147 32 3720 7750 76 82 241 247 1.636
14 13 99 0 30 89 86 22 17 90 -9 -6 93 0 29 101 99 31 99 -9 90 93 .09 100 -50 .904 1 27 11 7 0 3.355 2.301 8 7 414 80 3860 7720 71 81 253 263
15 372 460 0 276 90 88 23 381 252 153 137 236 0 95 102 99 29 99 153 252 137 236 .78 100 0 -1.316 -1.441 .442 .45 96 92 95 83 2.49 2.49 .402 .368 2.348 .402 .368 .336 534 509 333 80 4010 7720 71 81 268 278 -1.316
16 82 170 0 71 89 88 19 96 150 49 37 138 0 45 103 101 30 101 49 150 37 138 .34 90 0 -.97 -1.148 .528 .467 90 86 55 32 1.959 1.959 .51 .451 3.314 .51 .451 .36 145 119 265 52 4150 7730 72 81 282 291 -.97
17 10 98 0 25 89 88 20 15 100 -1 -3 98 0 32 104 101 32 101 -1 100 98 .03 100 -50 1.48 1.692 35 12 10 7 4.468 37.139 14 7 327 80 4300 7720 71 81 297 307
18 14 98 0 21 86 84 19 16 106 6 5 105 0 31 104 100 31 100 6 106 5 105 -1 100 -50 -1.485 1.366 1.857 37 12 25 6 2.667 2.667 .375 .357 4.532 .375 .357 -1 22 19 329 80 4440 7720 71 81 311 321 -1.415
19 133 218 0 62 86 85 18 130 178 82 73 169 0 61 100 96 29 96 82 178 73 169 .61 100 0 -.665 -.865 .571 .643 98 91 78 63 1.585 1.585 .631 .549 2.49 .631 .549 .682 212 206 331 80 4600 7730 72 82 327 337 -.665
20 72 159 0 54 88 87 20 79 158 62 56 152 0 51 99 96 28 96 62 158 56 152 .47 90 0 -.35 -.363 .913 .911 86 76 80 50 1.274 1.274 .785 .778 3.311 .785 .778 .84 141 128 262 52 4730 7730 72 81 340 349 -.35

Total number of rows: 43008

Table truncated, full table size 8418 Kbytes.




Supplementary data files not provided

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