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Sample GSM6240 Query DataSets for GSM6240
Status Public on Apr 15, 2004
Title AML 40
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 40
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=680640LaserPower=3.994.48
Lot batch = shco032
 
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 34 192 0 84 161 158 35 52 163 13 8 158 0 58 155 150 43 200 17 217 11 211 .28 100 -50 -1.672 .801 .695 50 33 33 8 4 3 .25 .235 4.317 .333 .314 .49 65 42 411 80 1890 7820 73 83 64 74 -1.585
2 53 218 0 100 166 165 34 67 150 -7 -9 148 0 53 165 157 51 209 -9 200 197 .2 100 -50 .364 .34 55 45 13 3 4.716 .269 60 44 336 80 2040 7820 73 83 79 89
3 780 951 0 493 175 171 45 858 207 42 47 212 0 70 172 165 55 220 56 276 63 283 .46 110 0 -3.937 -3.638 .077 .076 97 96 42 13 20.429 15.321 .049 .06 2.19 .065 .08 .057 900 827 364 80 2180 7830 73 84 92 103 -3.937
4 1988 2163 0 1409 183 175 61 2150 1965 1798 1743 1910 0 960 177 167 60 223 2397 2620 2324 2547 .96 80 0 .157 .225 .895 .834 96 96 100 100 1.196 .897 .836 .877 1.569 1.115 1.169 .772 3948 3731 243 52 2340 7850 77 85 110 118 .157
5 396 580 0 270 191 184 52 335 643 453 433 623 0 398 199 190 55 253 604 857 577 831 .89 70 0 .85 .544 1.035 1.245 84 71 75 68 .74 .555 1.352 1.093 2.099 1.803 1.458 1.41 788 829 194 32 2490 7840 76 83 125 132 .85
6 8 180 0 53 176 172 39 11 207 34 28 201 0 66 179 173 64 231 45 276 37 268 .18 100 -50 2.222 1.408 1.73 28 6 33 7 .324 .243 3.091 3.5 3.708 4.121 4.667 .042 45 36 377 80 2620 7820 73 83 137 147 2.043
7 63 218 0 79 162 155 51 50 4150 3988 4268 4430 0 2297 166 162 68 216 5317 5533 5691 5907 .61 80 0 6.733 6.497 46.73 44.955 53 26 100 100 .013 .009 79.76 67.746 1.635 106.347 90.328 62.689 4038 4331 263 52 2780 7830 75 83 154 162 6.733
8 2517 2704 0 1083 275 187 316 2255 1517 1355 1417 1579 0 662 195 162 175 216 1807 2023 1889 2105 .94 70 0 -.32 -.414 .603 .599 93 87 93 93 1.664 1.248 .601 .563 1.379 .801 .751 .579 3610 3934 181 32 2930 7830 75 82 169 176 -.32
9 298 532 0 768 293 234 242 430 1596 1421 1143 1318 0 1042 219 175 179 233 1895 2128 1524 1757 .73 110 0 2.14 2.354 4.513 4.093 61 27 93 86 .303 .227 3.305 3.836 2.186 4.406 5.114 1.603 1851 1441 454 80 3060 7840 74 85 180 191 2.14
10 97 307 0 212 242 210 128 123 253 99 69 223 0 148 181 154 121 205 132 337 92 297 .66 60 -100 -.076 .714 .597 43 9 34 9 1.242 .932 .805 .711 2.244 1.073 .948 .556 222 166 146 32 3220 7850 78 84 199 205 .102
11 623 820 0 438 208 197 70 615 319 170 162 311 0 150 159 149 70 199 227 425 216 415 .79 120 0 -1.44 -1.528 .327 .29 88 82 73 53 3.618 2.713 .276 .26 2.482 .369 .347 .281 785 785 526 120 3360 7830 73 85 210 222 -1.44
12 419 601 0 290 197 182 98 413 309 155 157 311 0 119 156 154 51 205 207 412 209 415 .73 70 0 -.999 -1.001 .354 .313 87 75 81 62 2.665 1.998 .375 .375 1.925 .5 .5 .328 568 576 186 32 3520 7830 75 82 228 235 -.999
13 163 355 0 153 210 192 88 167 256 95 95 256 0 96 165 161 51 215 127 341 127 341 .55 100 0 -.399 -.364 .634 .609 65 47 63 46 1.758 1.318 .569 .583 2.602 .758 .777 .358 262 258 283 80 3650 7850 76 86 240 250 -.399
14 -4 185 0 74 200 189 63 13 141 -9 -14 136 0 54 162 150 60 200 -12 188 181 .23 100 -50 .992 .829 23 8 11 2 3.643 .353 4 -18 319 80 3800 7820 73 83 255 265
15 1162 1330 0 724 175 168 50 1246 813 671 615 757 0 432 148 142 44 189 895 1084 820 1009 .94 100 0 -.478 -.503 .502 .501 96 95 96 95 1.857 1.393 .539 .529 1.765 .718 .706 .536 1917 1777 298 80 3940 7830 74 84 269 279 -.478
16 342 503 0 263 164 161 34 337 254 108 95 241 0 106 149 146 46 195 144 339 127 321 .71 100 0 -1.227 -1.433 .326 .338 81 78 67 51 3.12 2.34 .32 .278 2.92 .427 .37 .304 445 437 291 80 4090 7840 75 85 284 294 -1.227
17 12 176 0 61 164 164 32 9 151 5 -2 144 0 57 147 146 42 195 7 201 192 .15 100 -50 1.044 .863 30 13 26 10 1.8 1.35 .556 4.525 .741 1.536 14 10 333 80 4240 7820 73 83 299 309 -.433
18 -3 160 0 47 162 163 33 -4 139 -7 -18 128 0 54 146 146 47 195 -9 185 171 .06 100 -50 1.232 1.557 20 3 13 5 3.93 10.802 -11 -21 311 80 4390 7820 73 83 314 324
19 204 355 0 174 152 151 29 204 254 108 102 248 0 95 147 146 47 195 144 339 136 331 .63 110 0 -.503 -.585 .54 .579 86 77 70 55 1.889 1.417 .529 .5 2.293 .706 .667 .488 312 306 381 80 4520 7830 73 84 326 337 -.503
20 76 225 0 111 149 149 31 105 231 93 74 212 0 119 141 138 41 184 124 308 99 283 .62 100 0 .24 .377 .919 .847 72 56 60 47 1.129 .847 .886 .974 3.17 1.181 1.298 1.028 198 150 305 80 4680 7840 75 85 343 353 .24

Total number of rows: 43008

Table truncated, full table size 8711 Kbytes.




Supplementary data files not provided
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