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Sample GSM6284 Query DataSets for GSM6284
Status Public on Apr 15, 2004
Title AML 112
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 112
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=730640LaserPower=3.984.48
Lot batch = shcz228
 
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 48 81 0 30 35 33 10 53 262 226 236 272 0 117 42 36 20 41 257 298 268 309 .8 90 0 2.277 2.482 4.285 4.519 94 90 96 92 .235 .206 4.264 4.917 1.878 4.846 5.587 4.982 279 284 356 52 2500 7600 31 40 33 42 2.277
2 409 442 0 249 34 33 10 395 146 110 93 129 0 89 40 36 17 41 125 166 106 147 .9 80 0 -1.66 -1.952 .264 .289 100 100 82 75 3.591 3.16 .278 .227 2.034 .316 .258 .288 505 502 258 52 2650 7600 32 40 49 57 -1.66
3 179 211 0 135 33 32 9 215 206 171 132 167 0 120 38 35 15 40 194 234 150 190 .92 60 0 -.146 -.255 .749 .874 100 96 100 87 1.257 1.106 .795 .737 1.72 .904 .838 .822 386 311 164 32 2790 7600 33 39 64 70 -.146
4 66 99 0 46 35 33 17 69 163 127 102 138 0 104 41 36 20 41 144 185 116 157 .66 80 -100 .812 1.765 1.691 88 75 90 76 .543 .478 1.841 1.545 2.042 2.092 1.756 2.372 196 168 276 52 2950 7600 32 40 79 87 1.065
5 86 119 0 45 37 33 19 86 132 97 92 127 0 61 42 35 20 40 110 150 105 144 .73 80 -100 .282 1.182 1.075 94 86 90 84 .887 .78 1.128 1.07 1.87 1.282 1.216 1.364 183 178 221 52 3080 7610 33 41 92 100 .358
6 17 50 0 43 34 33 10 36 54 16 12 50 0 32 42 38 19 43 18 61 14 57 .44 100 -50 -.318 .868 .711 56 47 32 11 2.25 1.98 .444 .706 4.095 .505 .802 .736 52 29 407 80 3230 7600 31 41 106 116 -.986
7 82 116 0 56 35 34 10 87 214 176 134 172 0 160 43 38 22 43 200 243 152 195 .83 70 0 1.201 .893 1.57 1.685 96 90 87 75 .494 .435 2.023 1.634 2.088 2.299 1.857 2.681 263 216 212 32 3370 7610 33 40 121 128 1.201
8 51 86 0 39 37 35 11 55 55 20 12 47 0 24 46 35 46 40 23 63 14 53 .23 60 0 -1.275 -1.903 .423 .487 84 78 21 0 2.75 2.42 .364 .235 3.99 .413 .267 .295 75 63 160 32 3520 7590 32 38 137 143 -1.275
9 81 114 0 43 35 33 14 86 67 34 22 55 0 31 38 33 16 38 39 76 25 63 .28 50 0 -1.154 -1.696 .315 .314 91 91 75 41 2.529 2.226 .395 .272 3.649 .449 .309 .234 120 103 104 12 3670 7600 33 38 152 157 -1.154
10 58 92 0 28 36 34 12 63 50 14 6 42 0 30 40 36 18 41 16 57 7 48 .13 90 0 -1.986 -3.089 .357 .385 98 96 34 19 4.5 3.96 .222 .103 3.089 .253 .118 .222 77 64 367 52 3810 7610 32 41 164 173 -1.986
11 386 425 0 127 44 39 20 347 103 63 61 101 0 36 43 40 19 45 72 117 69 115 .7 50 0 -2.277 -2.477 .2 .24 100 100 91 83 5.508 4.847 .182 .158 1.545 .206 .18 .164 410 447 90 12 3960 7580 31 36 181 186 -2.277
12 252 285 0 207 35 33 10 297 283 244 228 267 0 166 43 39 18 44 277 322 259 303 .93 70 0 -.099 .04 .865 .855 96 93 100 96 1.217 1.071 .822 .905 1.888 .934 1.028 .805 541 480 226 32 4100 7590 31 38 194 201 -.099
13 131 164 0 61 34 33 8 120 200 164 159 195 0 131 41 36 19 41 186 227 181 222 .89 60 0 .635 .464 1.044 1.226 100 100 87 81 .732 .644 1.367 1.214 1.946 1.553 1.379 1.683 284 290 164 32 4240 7600 33 39 209 215 .635
14 49 83 0 22 36 34 9 51 56 19 4 41 0 35 42 37 19 42 22 64 5 47 .18 50 0 -1.24 -3.43 .452 .405 91 91 33 25 2.684 2.362 .373 .082 7.55 .423 .093 1.551 70 53 104 12 4380 7610 34 39 223 228 -1.24
15 50 83 0 41 34 33 8 60 1449 1412 1218 1255 0 939 41 37 17 42 1605 1647 1384 1426 .89 80 0 4.741 4.791 22.796 22.011 94 90 100 100 .042 .037 23.533 24.36 1.713 26.742 27.682 26.012 1472 1268 298 52 4540 7600 32 40 238 246 4.741
16 485 518 0 309 35 33 11 497 654 616 554 592 0 411 43 38 19 43 700 743 630 673 .94 80 0 .494 .376 1.301 1.217 98 98 100 96 .807 .71 1.239 1.142 1.816 1.408 1.298 1.294 1113 1039 277 52 4690 7600 32 40 253 261 .494
17 143 178 0 70 36 35 11 138 1091 1052 889 928 0 542 45 39 22 44 1195 1240 1010 1055 .93 90 0 3.115 2.821 7.726 7.402 96 94 100 100 .131 .115 7.623 6.217 1.422 8.663 7.065 8.13 1190 1032 332 52 4840 7610 32 41 267 276 3.115
18 78 114 0 40 37 36 10 90 57 19 14 52 0 26 43 38 20 43 22 65 16 59 .3 70 0 -2.06 -2.294 .265 .335 100 100 43 25 4.737 4.168 .211 .179 2.577 .24 .204 .19 109 92 214 32 4980 7600 32 39 282 289 -2.06
19 102 137 0 124 37 35 12 158 93 58 48 83 0 56 42 35 20 40 66 106 55 94 .69 60 0 -1.261 -.903 .366 .399 96 90 71 53 2.724 2.397 .367 .471 2.15 .417 .535 .338 216 150 160 32 5120 7590 32 38 297 303 -1.261
20 172 206 0 91 35 34 9 169 120 81 55 94 0 74 42 39 17 44 92 136 63 107 .76 70 0 -.877 -1.46 .37 .405 100 93 81 68 2.086 1.836 .479 .32 2.405 .545 .363 .529 250 227 227 32 5270 7600 32 39 311 318 -.877

Total number of rows: 43008

Table truncated, full table size 8600 Kbytes.




Supplementary data files not provided

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