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Sample GSM6239 Query DataSets for GSM6239
Status Public on Apr 15, 2004
Title AML 65
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 65
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=670640LaserPower=3.994.46
Lot batch = shco031
 
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 79 258 0 119 192 179 63 58 202 58 61 205 0 77 147 144 47 176 71 246 74 250 .42 60 0 .286 -.087 .568 .587 56 25 53 28 1 .82 1 .772 2.389 1.22 .942 .679 116 140 167 32 1770 7730 66 72 54 60 .286
2 180 377 0 122 223 197 91 156 164 25 25 164 0 56 141 139 48 170 30 200 30 200 .44 50 0 -2.355 -2.562 .284 .34 83 50 33 16 6.24 5.117 .16 .139 2.477 .195 .169 .239 181 205 104 12 1890 7710 64 69 66 71 -2.355
3 1179 1364 0 550 201 185 78 1045 151 1 5 155 0 52 153 150 46 183 1 184 6 189 .32 90 0 -9.743 -7.595 .082 .042 86 86 19 3 1045 856.9 .001 .004 6.835 .001 .005 .025 1046 1184 334 52 2040 7710 62 71 79 88 -9.743
4 1636 1821 0 1463 197 185 75 1625 1982 1829 1967 2120 0 1331 158 153 46 187 2230 2417 2399 2585 .94 90 0 .457 .552 1.44 1.057 75 75 100 96 .888 .729 1.126 1.202 2.431 1.373 1.466 1.01 3454 3603 308 52 2200 7730 64 73 95 104 .457
5 419 594 0 185 197 175 85 396 399 245 190 344 0 163 167 154 65 188 299 487 232 420 .77 50 0 -.406 -.855 .571 .549 91 91 91 83 1.616 1.325 .619 .453 1.852 .754 .553 .635 641 609 98 12 2370 7710 64 69 114 119 -.406
6 13 188 0 60 179 175 39 4 156 2 -12 142 0 61 161 154 56 188 2 190 173 .3 100 -50 1.593 1.254 33 5 22 5 2 1.64 .5 2.993 .61 2.439 6 1 362 80 2500 7710 62 72 125 135 -.714
7 191 375 0 184 196 184 93 147 1775 1622 1764 1917 0 1099 163 153 66 187 1978 2165 2151 2338 .85 80 0 3.75 3.494 9.335 9.256 61 50 94 90 .091 .074 11.034 9.236 1.506 13.456 11.263 8.631 1769 1955 242 52 2650 7720 64 72 141 149 3.75
8 2959 3151 0 1612 282 192 441 2447 1524 1374 1524 1674 0 845 212 150 247 183 1676 1859 1859 2041 .95 70 0 -.546 -.671 .707 .571 78 75 87 78 1.781 1.46 .562 .515 2.159 .685 .628 .519 3821 4483 186 32 2800 7700 62 69 156 163 -.546
9 175 355 0 252 223 180 318 202 1990 1843 1807 1954 0 1357 177 147 181 179 2248 2427 2204 2383 .79 110 0 3.476 3.654 9.385 7.322 30 5 93 81 .11 .09 9.124 10.326 2.073 11.127 12.592 7.621 2045 1982 355 80 2930 7720 62 73 167 178 3.476
10 2 187 0 75 211 185 99 9 164 17 14 161 0 66 155 147 51 179 21 200 17 196 .28 100 -50 3.094 .898 .812 10 1 23 10 .529 .434 1.889 7 4.294 2.304 8.537 .66 26 16 311 80 3080 7710 62 72 183 193 1.204
11 646 906 0 517 680 260 2353 644 433 270 257 420 0 233 488 163 1710 199 329 528 313 512 .97 100 -100 -1.043 .469 .424 0 0 0 0 2.385 1.956 .419 .398 2.692 .511 .485 .741 914 903 304 80 3220 7710 62 72 197 207 -.968
12 46 277 0 281 594 231 2146 119 215 62 6 159 0 143 427 153 1558 187 76 262 7 194 .96 100 -100 -2.652 .449 .427 0 0 0 0 1.919 1.574 .521 .13 2.371 .635 .159 .594 181 52 369 80 3370 7700 61 71 212 222 -.654
13 42 227 0 165 200 185 91 83 172 33 27 166 0 64 148 139 51 170 40 210 33 202 .49 100 -100 -.351 .559 .529 35 25 36 16 2.515 2.062 .398 .643 4.307 .485 .784 .293 116 69 350 80 3520 7700 61 71 227 237 -1.044
14 7 181 0 90 252 174 375 18 154 10 3 147 0 58 167 144 102 176 12 188 4 179 .75 100 -100 -.936 .573 .62 0 0 7 0 1.8 1.476 .556 .429 3.809 .678 .523 .262 28 10 393 80 3670 7700 61 71 242 252 -.562
15 820 1010 0 1377 346 190 518 1363 536 385 408 559 0 382 194 151 135 184 470 654 498 682 .8 70 0 -1.538 -.721 .337 .292 56 46 59 53 3.54 2.903 .282 .498 2.026 .344 .607 .225 1748 1228 192 32 3820 7720 64 71 258 265 -1.538
16 228 423 0 362 223 195 102 295 255 103 137 289 0 112 160 152 52 185 126 311 167 352 .54 70 0 -1.232 -.449 .438 .386 59 53 65 59 2.864 2.349 .349 .601 2.567 .426 .733 .249 398 365 203 32 3960 7700 62 69 272 279 -1.232
17 22 199 0 148 199 177 92 44 154 5 4 153 0 62 158 149 53 182 6 188 5 187 .46 100 -50 -2.173 .494 .551 23 6 17 3 8.8 7.216 .114 .182 3.574 .139 .222 .276 49 26 345 80 4110 7700 61 71 286 296 -2.851
18 -12 157 0 72 181 169 77 -9 151 6 -1 144 0 62 150 145 50 177 7 184 176 .24 100 -50 .614 .635 8 2 16 7 3.285 1.504 -3 -13 299 80 4250 7700 61 71 300 310
19 248 420 0 243 190 172 92 248 204 60 60 204 0 88 151 144 49 176 73 249 73 249 .6 90 0 -1.761 -1.761 .337 .398 65 57 51 30 4.133 3.389 .242 .242 3.032 .295 .295 .226 308 308 307 52 4370 7710 62 71 312 321 -1.761
20 98 273 0 201 191 175 79 136 223 82 87 228 0 130 148 141 45 172 100 272 106 278 .73 80 0 -.444 .115 .578 .609 51 44 61 46 1.659 1.36 .603 .888 2.534 .735 1.083 .602 218 185 275 52 4540 7720 64 72 330 338 -.444

Total number of rows: 43008

Table truncated, full table size 8706 Kbytes.




Supplementary data files not provided
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