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Sample GSM6278 Query DataSets for GSM6278
Status Public on Apr 15, 2004
Title AML 83
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 83
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=740620LaserPower=4.255.01
Lot batch = shcz222
 
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 58 100 0 25 44 42 11 62 53 14 8 47 0 20 43 39 18 56 20 76 11 67 .09 70 0 -1.632 -2.343 .232 .315 96 96 37 15 4.429 3.1 .226 .138 2.536 .323 .197 .151 76 66 218 32 2090 7760 44 51 45 52 -1.632
2 642 682 0 356 42 40 11 562 106 67 51 90 0 60 44 39 19 56 96 151 73 129 .73 90 0 -2.554 -3.139 .127 .116 96 92 78 65 8.388 5.872 .119 .079 2.512 .17 .113 .109 629 693 317 52 2230 7770 44 53 58 67 -2.554
3 271 311 0 194 41 40 10 260 201 159 126 168 0 130 46 42 19 60 227 287 180 240 .9 80 0 -.195 -.59 .635 .644 92 92 86 82 1.635 1.145 .612 .465 2.258 .874 .664 .612 419 397 288 52 2380 7770 45 53 74 82 -.195
4 96 138 0 39 46 42 23 91 86 44 41 83 0 40 46 42 19 60 63 123 59 119 .56 60 0 -.534 -.713 .442 .506 90 84 65 53 2.068 1.448 .484 .427 2.193 .691 .61 .504 135 137 165 32 2520 7760 45 51 89 95 -.534
5 113 154 0 58 44 41 13 105 181 140 123 164 0 102 46 41 19 59 200 259 176 234 .76 70 0 .93 .637 1.333 1.393 90 90 87 81 .75 .525 1.333 1.088 1.735 1.905 1.555 1.592 245 236 214 32 2660 7760 44 51 102 109 .93
6 84 125 0 23 42 41 9 88 90 52 45 83 0 29 43 38 17 54 74 129 64 119 .63 50 0 -.244 -.386 .508 .565 100 100 83 66 1.692 1.185 .591 .536 2.145 .844 .765 .574 140 129 104 12 2820 7770 46 51 119 124 -.244
7 173 218 0 73 49 45 17 175 165 117 150 198 0 75 53 48 25 69 167 236 214 283 .78 50 0 -.066 .309 .645 .74 100 100 75 75 1.496 1.047 .669 .867 2.11 .955 1.239 .833 292 323 104 12 2950 7770 46 51 132 137 -.066
8 109 151 0 49 46 42 14 109 59 19 17 57 0 16 46 40 20 57 27 84 24 81 .13 50 0 -2.006 -2.166 .193 .181 100 91 41 8 5.737 4.016 .174 .156 2.487 .249 .223 .069 128 126 98 12 3080 7760 45 50 145 150 -2.006
9 66 109 0 29 46 43 14 66 114 74 72 112 0 34 43 40 18 57 106 163 103 160 .58 50 0 .68 .64 1.127 1.228 100 91 100 83 .892 .624 1.121 1.091 1.739 1.602 1.558 .834 140 138 94 12 3270 7770 46 51 164 169 .68
10 68 111 0 45 46 43 14 63 58 15 17 60 0 20 48 43 21 61 21 83 24 86 .18 60 0 -1.556 -1.485 .306 .373 78 75 34 6 4.2 2.94 .238 .25 2.848 .34 .357 .156 78 85 158 32 3370 7780 47 53 174 180 -1.556
11 405 446 0 223 45 41 21 345 153 113 116 156 0 76 46 40 20 57 161 219 166 223 .79 70 0 -1.096 -1.289 .371 .38 96 87 87 78 3.053 2.137 .328 .286 2.28 .468 .409 .322 458 521 226 32 3540 7760 44 51 190 197 -1.096
12 90 130 0 262 41 40 9 216 201 163 79 117 0 195 43 38 19 54 233 287 113 167 .9 80 -100 .327 .626 .703 90 84 69 61 1.325 .928 .755 .878 2.454 1.078 1.254 .725 379 169 288 52 3690 7780 46 54 205 213 .108
13 175 215 0 44 43 40 13 170 105 65 54 94 0 47 43 40 16 57 93 150 77 134 .66 50 0 -.872 -1.182 .318 .363 100 100 100 66 2.615 1.831 .382 .309 2.012 .546 .441 .456 235 229 104 12 3830 7770 46 51 220 225 -.872
14 3 41 0 18 40 38 9 8 52 10 4 46 0 24 46 42 20 60 14 74 6 66 .26 100 -50 .93 1.644 1.3 28 16 25 13 .8 .56 1.25 1.333 3.475 1.786 1.905 4.556 18 7 377 80 3980 7770 44 54 233 243 .837
15 38 76 0 57 40 38 7 60 262 219 161 204 0 193 46 43 19 61 313 374 230 291 .91 100 0 2.382 2.598 3.507 3.479 76 70 87 80 .274 .192 3.65 4.237 2.34 5.214 6.053 3.768 279 199 313 80 4130 7780 45 55 248 258 2.382
16 229 268 0 377 40 39 8 413 1211 1171 815 855 0 1003 46 40 20 57 1673 1730 1164 1221 .95 110 0 2.018 2.346 3.059 2.639 93 90 100 96 .353 .247 2.835 3.559 2.329 4.051 5.084 2.857 1584 1044 369 80 4270 7780 44 55 261 272 2.018
17 117 157 0 233 40 40 9 157 466 424 378 420 0 332 46 42 19 60 606 666 540 600 .7 80 0 1.948 2.206 3.285 3.122 80 78 90 80 .37 .259 2.701 3.231 2.327 3.858 4.615 2.299 581 495 248 52 4420 7780 46 54 278 286 1.948
18 14 54 0 37 41 40 9 29 52 12 7 47 0 23 46 40 20 57 17 74 10 67 .19 100 -50 -.485 .922 .872 57 45 35 11 2.417 1.692 .414 .5 4.798 .591 .714 .548 41 21 362 80 4570 7770 44 54 292 302 -.758
19 227 270 0 178 44 43 12 238 110 72 66 104 0 64 45 38 19 54 103 157 94 149 .73 60 0 -1.21 -1.268 .308 .261 87 87 68 59 3.306 2.314 .303 .291 3.169 .432 .415 .26 310 293 152 32 4700 7770 46 52 307 313 -1.21
20 330 373 0 116 53 43 33 274 165 121 139 183 0 69 49 44 23 63 173 236 199 261 .89 50 0 -.665 -.733 .459 .453 100 91 91 83 2.264 1.585 .442 .421 1.766 .631 .602 .49 395 469 98 12 4850 7760 45 50 322 327 -.665

Total number of rows: 43008

Table truncated, full table size 8519 Kbytes.




Supplementary data files not provided
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