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Sample GSM6251 Query DataSets for GSM6251
Status Public on Apr 15, 2004
Title AML 117
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 117
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=680610LaserPower=3.844.56
Lot batch = shco054
 
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 47 156 0 30 110 109 22 49 162 46 42 158 0 42 116 116 35 109 43 153 40 149 .28 70 0 -.175 -.246 .936 1 81 53 59 31 1.065 1.129 .939 .894 3.53 .886 .843 2.622 95 89 216 32 2150 6920 56 63 83 90 -.175
2 27 133 0 31 107 106 20 31 128 12 9 125 0 39 117 116 37 109 11 121 8 118 .1 100 -50 -1.669 1.173 1.09 63 35 31 6 2.583 2.738 .387 .333 4.208 .365 .314 7.091 43 36 437 80 2290 6910 54 64 96 106 -1.453
3 398 505 0 219 109 107 64 439 148 38 29 139 0 42 112 110 34 104 36 140 27 131 .44 110 0 -3.614 -3.863 .096 .12 100 98 42 25 11.553 12.246 .087 .073 2.46 .082 .069 .077 477 427 345 80 2460 6930 55 66 112 123 -3.614
4 488 592 0 503 105 104 19 610 310 203 188 295 0 131 108 107 31 101 192 292 177 278 .89 90 0 -1.671 -1.46 .386 .351 96 96 100 92 3.005 3.185 .333 .385 1.909 .314 .363 .281 813 676 270 52 2600 6920 55 64 127 136 -1.671
5 63 170 0 44 107 107 21 74 171 67 59 163 0 59 109 104 33 98 63 161 56 154 .49 50 0 -.227 -.179 .74 .755 91 75 66 33 1.104 1.171 .905 .937 2.62 .854 .883 1.429 141 122 104 12 2730 6920 57 62 142 147 -.227
6 65 173 0 31 109 108 20 54 132 25 26 133 0 35 112 107 35 101 24 125 25 125 .21 50 0 -1.195 -1.406 .976 1 75 75 41 8 2.16 2.29 .463 .4 1.927 .437 .377 3.549 79 91 94 12 2890 6930 58 63 158 163 -1.195
7 124 226 0 56 103 102 20 142 141 33 25 133 0 35 111 108 33 102 31 133 24 125 .38 90 0 -2.189 -2.394 .207 .245 100 100 38 17 4.303 4.561 .232 .202 2.599 .219 .19 .249 175 149 329 52 3030 6930 56 65 170 179 -2.189
8 533 633 0 307 102 100 19 600 478 369 325 434 0 190 109 109 34 103 348 451 307 409 .93 80 0 -.785 -.798 .627 .632 100 100 98 98 1.626 1.724 .615 .61 1.497 .58 .575 .599 969 858 227 52 3180 6930 57 65 186 194 -.785
9 96 194 0 58 101 98 20 111 405 298 265 372 0 195 110 107 33 101 281 382 250 351 .84 80 0 1.341 1.381 2.65 2.54 96 94 100 100 .372 .395 2.685 2.76 1.866 2.533 2.604 3.274 409 361 201 52 3330 6930 57 65 201 209 1.341
10 16 113 0 37 100 97 20 27 114 13 11 112 0 31 103 101 31 95 12 108 10 106 .13 100 -50 -.625 1.08 1.1 47 26 27 7 2.077 2.202 .481 .688 4.064 .454 .649 2.129 40 27 362 80 3460 6910 54 64 213 223 -1.139
11 400 500 0 153 102 100 20 403 304 201 194 297 0 90 108 103 38 97 190 287 183 280 .84 110 0 -1.088 -1.128 .472 .482 100 100 97 93 2.005 2.125 .499 .485 1.753 .471 .458 .47 604 594 476 80 3620 6930 55 66 228 239 -1.088
12 93 195 0 48 108 102 27 103 156 53 40 143 0 40 107 103 35 97 50 147 38 135 .52 50 0 -1.043 -1.301 .433 .467 100 100 50 33 1.943 2.06 .515 .43 2.604 .485 .406 .672 156 133 104 12 3770 6920 57 62 246 251 -1.043
13 97 198 0 52 104 101 20 113 163 58 57 162 0 38 111 105 33 99 55 154 54 153 .43 70 0 -1.046 -.851 .535 .593 100 96 71 34 1.948 2.065 .513 .588 1.979 .484 .554 .624 171 154 188 32 3910 6930 57 64 259 266 -1.046
14 17 116 0 31 104 99 29 22 111 3 2 110 0 33 112 108 33 102 3 105 2 104 .13 100 -50 -3.172 .694 .75 33 13 15 3 7.333 7.773 .136 .118 4.818 .129 .111 .519 25 19 352 80 4040 6910 54 64 271 281 -2.959
15 774 872 0 322 103 98 34 803 213 105 98 206 0 64 109 108 34 102 99 201 92 194 .75 90 0 -3.019 -3.066 .117 .136 100 100 86 67 7.648 8.106 .131 .127 2.041 .123 .119 .125 908 872 268 52 4200 6920 55 64 287 296 -3.019
16 167 264 0 99 102 97 29 190 160 58 55 157 0 44 108 102 31 96 55 151 52 148 .59 80 0 -1.796 -1.686 .301 .315 100 100 73 46 3.276 3.472 .305 .329 1.887 .288 .311 .276 248 222 201 52 4340 6930 57 65 302 310 -1.796
17 13 105 0 25 94 92 20 15 111 10 8 109 0 32 104 101 30 95 9 105 8 103 .08 100 -50 -.785 .984 1.333 37 20 27 6 1.5 1.59 .667 .615 3.643 .629 .581 13.351 25 21 362 80 4480 6910 54 64 315 325 -.669
18 57 148 0 29 94 91 20 58 136 37 38 137 0 31 99 99 31 93 35 128 36 129 .07 50 0 -.733 -.669 .478 .671 91 58 58 8 1.568 1.662 .638 .667 3.889 .602 .629 .513 95 95 92 12 4630 6930 58 63 332 337 -.733
19 268 363 0 89 98 95 20 272 171 72 64 163 0 47 102 99 32 93 68 161 60 154 .55 110 0 -2.002 -2.15 .229 .29 100 100 77 48 3.778 4.004 .265 .239 2.294 .25 .225 .217 344 332 382 80 4790 6930 55 66 345 356 -2.002
20 40 138 0 41 101 98 20 39 116 13 11 114 0 34 107 103 34 97 12 109 10 108 .21 100 -50 -1.947 .709 .719 65 48 27 6 3 3.18 .333 .275 3.546 .314 .259 1.511 52 51 339 80 4920 6910 54 64 359 369 -1.669

Total number of rows: 43008

Table truncated, full table size 8434 Kbytes.




Supplementary data files not provided

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