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Sample GSM6250 Query DataSets for GSM6250
Status Public on Apr 15, 2004
Title AML 27
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 27
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=680590LaserPower=3.634.56
Lot batch = shco053
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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 �m 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 �m 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 �m 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 10 95 0 28 86 85 16 15 103 11 7 99 0 38 97 92 39 108 13 121 8 116 .11 100 -50 -.28 1.178 1.144 40 26 16 7 1.364 1.159 .733 .7 3.859 .863 .824 7.875 26 17 452 80 2050 7390 50 60 72 82 -.213
2 13 99 0 20 89 86 26 16 106 10 5 101 0 35 102 96 35 113 12 125 6 119 .12 100 -50 -1.144 1.284 1.175 27 6 17 5 1.6 1.36 .625 .385 4.702 .735 .452 3.067 26 18 409 80 2200 7390 50 60 87 97 -.444
3 324 408 0 123 88 84 26 337 131 37 25 119 0 45 100 94 34 111 44 154 29 140 .3 100 0 -2.953 -3.462 .12 .128 100 100 42 20 9.108 7.742 .11 .077 2.621 .129 .091 .076 374 349 343 80 2370 7410 52 62 104 114 -2.953
4 566 648 0 404 84 82 15 626 409 308 274 375 0 186 104 101 35 119 362 481 322 441 .88 80 0 -.789 -.812 .53 .498 100 94 96 92 2.032 1.728 .492 .484 2.204 .579 .57 .449 934 840 274 52 2500 7410 53 61 118 126 -.789
5 83 177 0 41 123 94 160 73 167 60 59 166 0 28 130 107 127 126 71 196 69 195 .32 50 -100 -.258 .956 .877 0 0 0 0 1.217 1.034 .822 .711 2.542 .967 .836 .132 133 142 104 12 2670 7410 54 59 136 141 -.048
6 36 127 0 29 116 91 137 39 184 81 77 180 0 50 125 103 109 121 95 216 91 212 .47 60 -100 1.331 2.175 2.222 0 0 28 0 .481 .409 2.077 2.139 3.434 2.443 2.516 2.863 120 113 146 32 2790 7410 54 60 148 154 1.289
7 40 122 0 38 90 82 81 49 695 593 571 673 0 287 112 102 48 120 698 818 672 792 .69 90 0 3.832 4.07 12.919 12.685 15 1 100 96 .083 .07 12.102 14.275 1.999 14.238 16.794 13.026 642 611 296 52 2930 7410 52 61 160 169 3.832
8 616 697 0 440 82 81 15 633 685 585 563 663 0 313 110 100 47 118 688 806 662 780 .92 80 0 .121 .105 .952 .917 98 98 98 96 1.082 .92 .924 .914 2.101 1.087 1.075 .823 1218 1179 240 52 3090 7410 53 61 177 185 .121
9 86 167 0 52 81 81 15 94 653 553 476 576 0 318 102 100 32 118 651 768 560 678 .84 80 0 2.791 2.703 5.752 5.183 96 88 100 100 .17 .144 5.883 5.535 1.776 6.921 6.512 6.816 647 562 245 52 3230 7410 53 61 191 199 2.791
10 11 91 0 26 83 80 30 13 108 9 4 103 0 31 102 99 34 116 11 127 5 121 .11 100 -50 -1.225 2.039 2.028 25 5 17 3 1.444 1.228 .692 .364 4.268 .814 .428 16.948 22 15 399 80 3360 7390 50 60 203 213 -.296
11 230 310 0 84 82 80 32 238 153 63 59 149 0 51 97 90 33 106 74 180 69 175 .54 100 0 -1.683 -1.728 .249 .27 100 100 73 46 3.778 3.211 .265 .257 2.352 .311 .302 .236 301 289 320 80 3530 7410 52 62 220 230 -1.683
12 25 104 0 52 81 79 21 42 110 18 14 106 0 42 98 92 32 108 21 129 16 125 .26 100 -50 -.602 .915 .975 53 36 36 15 2.333 1.983 .429 .56 3.531 .504 .659 1.044 60 39 347 80 3650 7390 50 60 232 242 -.988
13 19 96 0 55 79 77 21 37 109 16 11 104 0 42 97 93 32 109 19 128 13 122 .26 100 -50 -.554 1.072 1.059 47 35 32 13 2.313 1.966 .432 .579 4.097 .509 .681 .822 53 30 342 80 3800 7390 50 60 247 257 -.975
14 10 88 0 23 78 78 15 15 106 12 6 100 0 31 97 94 31 111 14 125 7 118 -1 100 -50 -.503 1.424 1.463 42 16 27 8 1.25 1.063 .8 .6 6.109 .941 .706 -1 27 16 357 80 3940 7390 50 60 261 271 -.087
15 507 586 0 318 80 79 19 533 233 139 121 215 0 78 99 94 33 111 164 274 142 253 .78 90 0 -1.705 -1.833 .27 .266 100 100 98 84 3.835 3.259 .261 .239 1.853 .307 .281 .22 672 628 272 52 4110 7410 52 61 278 287 -1.705
16 157 237 0 75 82 80 21 173 160 67 65 158 0 56 100 93 34 109 79 188 76 186 .51 80 0 -1.134 -1.038 .386 .474 100 100 69 50 2.582 2.195 .387 .414 2.436 .456 .487 .368 240 222 199 52 4250 7410 53 61 293 301 -1.134
17 9 88 0 28 82 79 19 13 96 4 3 95 0 30 99 92 36 108 5 113 4 112 .03 100 -50 -1.35 1.276 1.142 32 11 11 3 3.25 2.763 .308 .333 4.286 .362 .392 .05 17 12 323 80 4380 7390 50 60 305 315 -1.466
18 14 93 0 22 81 79 16 18 102 7 0 95 0 32 98 95 32 112 8 120 0 112 .04 100 -50 1.101 1.034 45 18 16 3 2.571 2.186 .389 4.311 .458 24.352 25 14 362 80 4530 7390 50 60 320 330 -1.128
19 163 242 0 73 80 79 15 174 130 31 19 118 0 46 102 99 33 116 36 153 22 139 .3 100 0 -2.254 -2.866 .224 .239 100 100 41 25 5.613 4.771 .178 .117 2.719 .21 .137 .158 205 182 332 80 4700 7410 52 62 337 347 -2.254
20 19 97 0 25 80 78 17 20 104 6 0 98 0 37 101 98 33 115 7 122 0 115 .08 100 -50 1.232 1.113 52 18 22 6 3.333 2.833 .3 4.399 .353 10.492 26 19 336 80 4820 7390 50 60 349 359 -1.503

Total number of rows: 43008

Table truncated, full table size 8221 Kbytes.




Supplementary data files not provided

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