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Sample GSM6279 Query DataSets for GSM6279
Status Public on Apr 15, 2004
Title AML 99
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 99
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=4.254.82
Lot batch = shcz223
 
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
1 114 164 0 40 51 50 14 114 82 36 32 78 0 29 48 46 18 69 54 122 48 116 .46 70 0 -1.085 -1.255 .309 .358 96 96 71 43 3.167 2.122 .316 .281 2.387 .471 .419 .264 150 146 203 32 2150 7850 37 44 27 34 -1.085
2 238 286 0 335 49 48 12 364 2437 2392 1725 1770 0 2131 49 45 24 67 3570 3637 2575 2642 .98 100 0 3.294 3.435 6.933 6.654 95 86 100 100 .152 .102 6.571 7.248 1.566 9.808 10.818 6.558 2756 1963 357 80 2280 7860 37 47 39 49 3.294
3 311 360 0 329 49 49 12 390 230 186 173 217 0 151 49 44 19 66 278 343 258 324 .96 80 0 -.49 -.268 .533 .501 96 94 92 82 2.097 1.405 .477 .556 1.999 .712 .83 .453 576 484 266 52 2430 7850 37 45 55 63 -.49
4 42 91 0 77 50 49 13 66 637 593 320 364 0 595 47 44 17 66 885 951 478 543 .89 100 0 3.745 3.507 8.325 7.948 66 55 97 96 .111 .075 8.985 7.619 2.021 13.41 11.372 8.952 659 362 365 80 2580 7840 35 45 69 79 3.745
5 38 88 0 100 52 50 15 83 117 72 31 76 0 94 48 45 16 67 107 175 46 113 .88 100 0 .373 .284 .826 .889 75 57 65 48 1.153 .772 .867 .816 2.575 1.295 1.218 .901 155 69 351 80 2720 7850 36 46 83 93 .373
6 86 135 0 64 52 49 16 93 78 34 25 69 0 36 47 44 16 66 51 116 37 103 .65 60 0 -.874 -1.205 .376 .4 87 84 65 40 2.735 1.833 .366 .291 2.248 .546 .434 .37 127 111 165 32 2870 7840 37 43 100 106 -.874
7 99 148 0 144 50 49 12 148 231 184 112 159 0 171 49 47 16 70 275 345 167 237 .92 80 0 .892 .756 1.307 1.251 88 73 90 78 .804 .539 1.243 1.131 2.599 1.856 1.689 1.245 332 211 265 52 3020 7840 36 44 114 122 .892
8 29 77 0 56 50 48 13 50 54 10 6 50 0 20 46 44 14 66 15 81 9 75 .37 100 -50 -1.695 .341 .351 75 53 30 18 5 3.35 .2 .207 2.874 .299 .309 .2 60 35 419 80 3160 7840 35 45 127 137 -1.744
9 120 172 0 55 52 52 14 139 194 149 128 173 0 62 47 45 16 67 222 290 191 258 .81 50 0 .678 .671 1.064 1.051 100 100 100 100 .933 .625 1.072 1.067 1.522 1.6 1.592 1.06 288 248 98 12 3310 7840 37 42 144 149 .678
10 118 169 0 52 54 51 19 113 67 22 22 67 0 24 48 45 15 67 33 100 33 100 .37 70 0 -1.783 -1.845 .201 .208 96 93 56 31 5.136 3.441 .195 .186 2.923 .291 .278 .155 135 140 219 32 3450 7840 36 43 157 164 -1.783
11 345 394 0 353 51 49 14 410 106 62 45 89 0 66 48 44 17 66 93 158 67 133 .85 80 0 -2.148 -2.361 .202 .164 92 88 69 59 6.613 4.431 .151 .13 3.337 .226 .195 .15 472 390 286 52 3600 7840 36 44 172 180 -2.148
12 390 438 0 440 49 48 13 518 465 420 352 397 0 385 48 45 17 67 627 694 525 593 .98 80 0 .275 .43 .749 .788 94 94 96 88 1.233 .826 .811 .903 1.821 1.21 1.347 .838 938 742 274 52 3740 7840 36 44 186 194 .275
13 241 291 0 157 52 50 15 244 269 223 218 264 0 122 49 46 17 69 333 401 325 394 .91 60 0 .448 .433 .985 .973 100 93 100 96 1.094 .733 .914 .905 1.763 1.364 1.35 .851 467 459 170 32 3890 7840 37 43 202 208 .448
14 12 59 0 33 49 47 13 21 56 10 7 53 0 24 50 46 19 69 15 84 10 79 .31 100 -50 -.2 .72 .645 48 31 26 8 2.1 1.407 .476 .583 3.313 .711 .871 .684 31 19 432 80 4040 7840 35 45 215 225 -.493
15 178 225 0 90 48 47 13 157 1138 1094 1153 1197 0 561 49 44 19 66 1633 1699 1721 1787 .94 90 0 3.379 3.273 7.393 7.043 92 88 100 100 .144 .096 6.968 6.478 1.623 10.4 9.668 7.075 1251 1331 312 52 4190 7840 35 44 230 239 3.379
16 916 964 0 509 50 48 13 920 1902 1855 1899 1946 0 1107 51 47 20 70 2769 2839 2834 2904 .98 90 0 1.589 1.63 1.986 2.041 100 100 100 100 .496 .332 2.016 2.073 1.51 3.009 3.094 2.084 2775 2815 317 52 4330 7840 35 44 244 253 1.589
17 195 244 0 166 51 49 14 218 985 938 907 954 0 658 55 47 34 70 1400 1470 1354 1424 .96 90 0 2.683 2.795 4.799 4.41 98 88 100 100 .232 .156 4.303 4.651 1.72 6.422 6.942 4.273 1156 1102 320 52 4470 7820 33 42 258 267 2.683
18 100 151 0 55 53 51 16 114 66 20 19 65 0 18 49 46 14 69 30 99 28 97 .23 50 0 -1.933 -1.818 .228 .18 91 91 58 16 5.7 3.819 .175 .19 3.205 .262 .284 .097 134 119 98 12 4610 7830 36 41 274 279 -1.933
19 378 429 0 269 55 51 20 389 163 116 121 168 0 85 50 47 17 70 173 243 181 251 .89 60 0 -1.168 -1.066 .296 .336 100 96 87 78 3.353 2.247 .298 .32 1.825 .445 .478 .284 505 499 170 32 4770 7830 36 42 290 296 -1.168
20 291 339 0 207 50 48 13 310 212 168 130 174 0 139 49 44 17 66 251 316 194 260 .91 60 0 -.306 -.585 .437 .5 96 96 90 81 1.845 1.236 .542 .447 1.741 .809 .667 .57 478 421 165 32 4920 7830 36 42 305 311 -.306

Total number of rows: 43008

Table truncated, full table size 8677 Kbytes.




Supplementary data files not provided
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