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Sample GSM6285 Query DataSets for GSM6285
Status Public on Apr 15, 2004
Title AML 25
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 25
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=690650LaserPower=3.975.01
Lot batch = shcz110
 
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 47 78 0 34 33 31 6 51 78 45 34 67 0 37 36 33 11 47 64 111 49 96 .64 80 0 .334 .047 .912 .931 90 86 84 65 1.133 .793 .882 .723 2.908 1.261 1.033 1.016 96 81 289 52 1550 8350 39 47 19 27 .334
2 345 377 0 348 34 32 8 451 335 302 211 244 0 216 37 33 14 47 431 479 301 349 .92 60 0 -.064 -.195 .827 .744 100 96 96 96 1.493 1.045 .67 .612 2.19 .957 .874 .616 753 556 170 32 1700 8350 40 46 35 41 -.064
3 198 229 0 221 32 31 7 255 108 75 62 95 0 61 36 33 11 47 107 154 89 136 .74 60 0 -1.251 -1.161 .337 .307 100 96 93 84 3.4 2.38 .294 .313 2.607 .42 .447 .221 330 260 170 32 1840 8350 40 46 49 55 -1.251
4 76 109 0 69 34 33 8 90 167 131 93 129 0 120 39 36 14 51 187 239 133 184 .83 70 0 1.056 .806 1.213 1.505 93 93 84 71 .687 .481 1.456 1.224 2.775 2.079 1.748 1.69 221 169 232 32 1980 8350 39 46 62 69 1.056
5 88 122 0 73 37 34 11 93 90 55 43 78 0 53 40 35 15 50 79 129 61 111 .74 70 0 -.243 -.519 .532 .543 87 84 75 59 1.691 1.184 .591 .489 2.402 .845 .698 .611 148 131 216 32 2150 8340 38 45 79 86 -.243
6 118 151 0 48 35 33 9 113 101 63 54 92 0 64 42 38 16 54 90 144 77 131 .62 50 0 -.328 -.613 .549 .554 100 100 75 66 1.794 1.256 .558 .458 1.962 .796 .654 .708 176 172 98 12 2270 8340 39 44 92 97 -.328
7 70 102 0 111 34 32 7 124 198 166 98 130 0 140 36 32 12 46 237 283 140 186 .91 60 0 .935 1 1.419 1.235 100 93 100 96 .747 .523 1.339 1.4 1.827 1.912 2 1.323 290 168 170 32 2420 8350 40 46 107 113 .935
8 50 83 0 46 34 33 7 66 75 41 35 69 0 41 37 34 12 49 59 107 50 99 .63 70 0 -.172 0 .471 .598 93 93 75 59 1.61 1.127 .621 .7 3.445 .887 1 .692 107 85 232 32 2560 8350 39 46 120 127 -.172
9 69 99 0 39 32 30 6 70 148 115 100 133 0 81 36 33 11 47 164 211 143 190 .83 60 0 1.231 1.05 1.463 1.399 100 96 93 84 .609 .426 1.643 1.449 1.964 2.347 2.07 2.003 185 169 164 32 2720 8350 40 46 137 143 1.231
10 60 90 0 46 32 30 7 66 55 23 21 53 0 16 36 32 11 46 33 79 30 76 .38 80 0 -1.006 -1 .385 .356 94 92 75 46 2.87 2.009 .348 .35 2.949 .498 .5 .199 89 81 273 52 2860 8350 39 47 150 158 -1.006
11 245 276 0 235 32 31 7 278 82 48 38 72 0 48 37 34 11 49 69 117 54 103 .7 60 0 -2.019 -2.174 .229 .175 90 90 78 65 5.792 4.054 .173 .155 3.352 .247 .222 .138 326 283 164 32 3000 8350 40 46 165 171 -2.019
12 333 364 0 357 32 31 6 390 312 279 209 242 0 249 37 33 11 47 399 446 299 346 .94 60 0 .031 -.157 .715 .743 100 96 90 90 1.398 .978 .715 .628 2.138 1.022 .897 .692 669 542 165 32 3150 8350 40 46 180 186 .031
13 188 222 0 70 35 34 8 182 198 162 187 223 0 74 41 36 15 51 231 283 267 319 .85 50 0 .347 .507 .844 1.012 100 100 100 100 1.123 .786 .89 .995 1.741 1.272 1.421 .975 344 375 98 12 3290 8340 39 44 194 199 .347
14 28 58 0 31 32 30 7 32 56 22 16 50 0 29 38 34 12 49 31 80 23 71 .31 60 0 -.026 -.293 1.181 1 75 62 56 37 1.455 1.018 .688 .571 5.171 .982 .816 .862 54 44 160 32 3440 8340 39 45 209 215 -.026
15 37 67 0 39 36 30 40 47 598 564 376 410 0 539 46 34 73 49 806 854 537 586 .62 80 0 4.1 3.86 10.202 10.859 46 21 88 78 .083 .058 12 10.162 2.692 17.143 14.517 14.686 611 413 270 52 3590 8350 39 47 223 231 4.1
16 222 253 0 327 32 31 7 338 659 625 466 500 0 606 37 34 12 49 893 941 666 714 .89 80 0 1.401 1.584 1.809 1.592 90 86 92 86 .541 .379 1.849 2.099 2.721 2.642 2.999 1.982 963 688 276 52 3730 8340 38 46 237 245 1.401
17 95 126 0 103 32 31 6 116 638 604 386 420 0 553 37 34 11 49 863 911 551 600 .87 80 0 2.895 2.537 4.863 4.625 96 88 96 96 .192 .134 5.207 4.063 2.817 7.438 5.805 5.995 720 481 288 52 3890 8350 39 47 253 261 2.895
18 74 104 0 42 32 30 6 78 54 19 18 53 0 22 36 35 9 50 27 77 26 76 .39 70 0 -1.523 -1.525 .333 .299 100 96 62 43 4.105 2.874 .244 .243 2.494 .348 .347 .19 97 92 214 32 4030 8340 38 45 267 274 -1.523
19 218 248 0 173 32 30 6 248 186 150 143 179 0 101 38 36 11 51 214 266 204 256 .87 60 0 -.211 -.094 .633 .567 96 96 93 84 1.653 1.157 .605 .656 2.741 .864 .937 .56 398 361 170 32 4170 8340 39 45 282 288 -.211
20 180 212 0 139 33 32 6 206 214 179 194 229 0 121 38 35 13 50 256 306 277 327 .88 60 0 .312 .623 .853 .852 100 100 96 87 1.151 .806 .869 1.078 1.953 1.241 1.54 .852 385 374 170 32 4320 8340 39 45 297 303 .312

Total number of rows: 43008

Table truncated, full table size 8673 Kbytes.




Supplementary data files not provided
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