NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6247 Query DataSets for GSM6247
Status Public on Apr 15, 2004
Title AML 116
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 116
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=680620LaserPower=3.664.57
Lot batch = shco048
 
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 44 143 0 22 104 99 25 42 101 22 14 93 0 44 88 79 31 90 25 115 16 106 .19 50 0 -.748 -1.468 .813 .732 83 41 25 16 1.909 1.68 .524 .318 2.844 .595 .362 2.81 64 58 104 12 1940 7670 72 77 63 68 -.748
2 16 112 0 30 98 96 21 22 86 3 1 84 0 28 86 83 27 94 3 98 1 95 .12 100 -50 -3.816 .73 .667 46 23 16 8 7.333 6.453 .136 .063 5.94 .155 .071 2.044 25 17 458 80 2080 7670 70 80 75 85 -2.69
3 272 369 0 114 99 97 20 290 117 32 25 110 0 41 87 85 28 97 36 133 28 125 .48 100 0 -2.995 -3.259 .126 .156 100 100 45 27 9.063 7.975 .11 .092 2.226 .125 .104 .116 322 297 319 80 2260 7680 71 81 93 103 -2.995
4 415 513 0 363 101 98 20 513 302 220 198 280 0 169 85 82 27 93 250 343 225 318 .83 80 0 -1.037 -.883 .413 .423 98 96 94 84 2.332 2.052 .429 .477 1.963 .487 .542 .399 733 613 224 52 2390 7680 72 80 107 115 -1.037
5 45 142 0 27 97 97 17 53 129 45 44 128 0 32 86 84 24 95 51 147 50 145 .3 50 0 -.052 .152 .764 1.074 91 75 66 50 1.178 1.036 .849 .978 3.127 .965 1.111 2.052 98 89 104 12 2540 7690 74 79 123 128 -.052
6 46 147 0 26 102 101 24 46 110 28 28 110 0 30 87 82 31 93 32 125 32 125 .27 60 0 -.532 -.532 .681 .68 84 43 34 15 1.643 1.446 .609 .609 3.185 .692 .692 .743 74 74 147 32 2680 7690 74 80 137 143 -.532
7 66 162 0 48 95 96 19 64 613 532 516 597 0 303 84 81 28 92 605 697 586 678 .78 100 0 3.24 3.151 8.897 8.549 78 68 100 98 .12 .106 8.313 7.818 2.051 9.446 8.884 9.298 596 582 314 80 2840 7690 72 82 151 161 3.24
8 829 919 0 470 93 90 22 895 976 897 824 903 0 424 81 79 25 90 1019 1109 936 1026 .94 80 0 .188 .176 1.039 1.07 100 100 100 100 .998 .878 1.002 .994 1.5 1.139 1.13 .962 1792 1653 195 52 2980 7690 73 81 166 174 .188
9 84 171 0 68 89 87 20 87 370 288 247 329 0 191 85 82 27 93 327 420 281 374 .79 80 0 1.911 1.74 3.523 3.325 80 73 100 94 .302 .266 3.31 2.94 2.238 3.762 3.341 3.725 375 331 202 52 3120 7690 73 81 180 188 1.911
10 8 94 0 21 87 86 18 11 87 7 3 83 0 32 84 80 27 91 8 99 3 94 .22 100 -50 -1.231 1.477 1.462 28 12 20 8 1.571 1.383 .636 .375 3.303 .723 .426 3.652 18 11 396 80 3260 7670 70 80 193 203 -.468
11 247 332 0 73 87 85 21 257 162 79 69 152 0 54 85 83 27 94 90 184 78 173 .67 110 0 -1.517 -1.655 .274 .279 100 100 87 65 3.253 2.863 .307 .279 1.967 .349 .317 .331 336 316 408 80 3420 7680 70 81 208 219 -1.517
12 64 152 0 44 90 88 19 67 114 35 40 119 0 34 80 79 26 90 40 130 45 135 .27 60 0 -.752 -.494 .961 .778 87 68 59 37 1.914 1.685 .522 .625 2.854 .594 .71 .514 102 104 164 32 3560 7680 73 79 225 231 -.752
13 69 161 0 46 98 92 30 73 127 50 47 124 0 31 80 77 22 88 57 144 53 141 .08 50 0 -.362 -.37 .791 .643 83 58 66 50 1.46 1.285 .685 .681 3.93 .778 .774 .148 123 116 104 12 3700 7690 74 79 239 244 -.362
14 15 102 0 21 90 87 22 16 82 0 -1 81 0 25 86 82 32 93 0 93 92 .04 100 -50 1.093 .895 36 10 11 1 4.376 11.144 16 14 395 80 3850 7670 70 80 252 262
15 632 726 0 333 100 94 32 630 225 142 134 217 0 81 91 83 42 94 161 256 152 247 .84 70 0 -1.965 -2.053 .232 .246 100 100 90 78 4.437 3.904 .225 .212 1.607 .256 .241 .201 772 766 183 32 4000 7680 72 79 268 275 -1.965
16 128 219 0 71 96 91 30 146 185 99 61 147 0 104 90 86 35 98 113 210 69 167 .43 80 -100 -.885 .532 .592 100 92 73 48 1.475 1.298 .678 .477 2.458 .771 .542 .128 245 189 226 52 4140 7690 73 81 282 290 -.376
17 15 100 0 25 87 85 19 19 92 10 5 87 0 29 86 82 27 93 11 105 6 99 .22 100 -50 -1.401 1.082 1.038 41 16 28 6 1.9 1.672 .526 .333 3.725 .598 .379 2.341 29 20 312 80 4290 7670 70 80 296 306 -.742
18 21 109 0 23 92 88 27 19 86 3 1 84 0 29 88 83 31 94 3 98 1 95 .03 100 -50 -4.208 .511 .42 40 3 15 2 6.333 5.573 .158 .048 3.681 .179 .054 12.395 22 22 303 80 4430 7670 70 80 310 320 -2.479
19 216 307 0 79 97 91 37 230 194 109 108 193 0 66 89 85 33 97 124 220 123 219 .68 110 0 -.893 -.816 .427 .475 100 97 87 72 2.11 1.857 .474 .5 2.053 .539 .568 .489 339 324 380 80 4580 7680 70 81 324 335 -.893
20 19 107 0 26 90 88 22 25 102 18 12 96 0 36 86 84 29 95 20 116 14 109 .19 100 -50 -.479 .962 .9 48 27 31 11 1.389 1.222 .72 .632 3.736 .818 .718 2.895 43 31 328 80 4730 7670 70 80 340 350 -.29

Total number of rows: 43008

Table truncated, full table size 8382 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap