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Sample GSM6243 Query DataSets for GSM6243
Status Public on Apr 15, 2004
Title AML 38
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 38
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=670600LaserPower=3.324.45
Lot batch = shco039
 
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 -2 73 0 22 107 75 250 1 98 -13 -18 93 0 37 148 111 268 134 -16 118 112 .95 100 -50 2.117 2.087 0 0 0 0 2.889 .831 -12 -20 378 80 1990 7900 53 63 66 76
2 14 91 0 39 79 77 17 19 111 1 -7 103 0 61 113 110 33 133 1 134 124 .39 100 -50 1.562 1.929 40 20 23 8 19 15.77 .053 3.645 .063 2.272 20 7 312 80 2130 7900 53 63 80 90 -3.979
3 72 150 0 102 79 78 16 101 110 -2 -3 109 0 36 113 112 30 135 -2 133 131 .13 100 0 .451 .328 76 68 20 3 5.055 .061 99 69 301 80 2280 7910 54 64 95 105
4 97 176 0 281 81 79 17 205 215 103 73 185 0 136 114 112 32 135 124 259 88 223 .78 100 0 -.724 -.141 .622 .653 70 65 67 52 1.99 1.652 .502 .753 3.352 .605 .907 .44 308 170 296 80 2420 7910 54 64 109 119 -.724
5 8 87 0 47 81 79 17 22 110 1 -4 105 0 44 114 109 34 131 1 133 127 .21 100 -50 1.025 1.03 37 28 11 7 22 18.26 .045 4.38 .055 1.997 23 4 326 80 2570 7900 53 63 124 134 -4.191
6 0 79 0 18 81 79 17 -1 109 -4 -5 108 0 39 118 113 37 136 -5 131 130 .06 100 -50 1.472 1.6 16 1 12 6 3.167 24.722 -5 -5 346 80 2720 7900 53 63 139 149
7 -5 76 0 24 82 81 18 -3 472 349 337 460 0 320 132 123 71 148 420 569 406 554 .14 80 0 9.101 11.202 13 5 71 65 4.806 87.283 346 332 244 52 2870 7890 53 61 155 163
8 143 224 0 349 83 81 19 277 479 362 248 365 0 420 121 117 40 141 436 577 299 440 .82 80 0 .655 1.063 1.53 1.532 69 63 71 65 .765 .635 1.307 1.734 3.294 1.575 2.089 1.245 639 391 235 52 3020 7900 54 62 170 178 .655
9 17 96 0 56 82 79 22 30 367 254 156 269 0 307 116 113 34 136 306 442 188 324 .62 100 0 3.351 3.467 3.588 5.349 42 33 62 57 .118 .098 8.467 9.176 4.461 10.201 11.056 9.015 284 173 313 80 3160 7910 54 64 183 193 3.351
10 2 79 0 19 89 77 100 0 114 -4 -8 110 0 44 123 118 48 142 -5 137 133 .54 100 -50 2.229 2.491 0 0 15 1 2.564 .296 -4 -6 393 80 3300 7900 53 63 197 207
11 79 161 0 99 86 82 25 90 110 -3 -10 103 0 47 119 113 44 136 -4 133 124 .13 90 0 .594 .727 65 53 19 3 4.987 .222 87 69 289 52 3460 7900 53 62 213 222
12 7 86 0 54 82 79 21 23 103 -14 -16 101 0 33 120 117 35 141 -17 124 122 .08 100 -50 1.32 1.752 38 23 6 1 4.285 .33 9 -9 356 80 3600 7900 53 63 227 237
13 8 86 0 40 80 78 17 16 108 -10 -8 110 0 43 123 118 34 142 -12 130 133 .09 100 -50 1.1 1.692 40 26 16 5 4.218 6.75 6 0 320 80 3740 7900 53 63 241 251
14 0 79 0 21 86 79 57 -2 109 -7 -16 100 0 37 121 116 37 140 -8 131 120 .11 100 -50 1.64 1.75 1 0 13 2 2.92 12.715 -9 -16 350 80 3890 7900 53 63 256 266
15 140 222 0 313 90 82 61 240 116 -5 -8 113 0 45 126 121 37 146 -6 140 136 .15 80 0 .354 .352 53 50 19 7 7.623 .032 235 132 211 52 4040 7920 56 64 272 280
16 18 99 0 51 90 81 63 27 122 2 3 123 0 43 127 120 45 145 2 147 4 148 .12 100 -50 -2.316 .912 .966 20 5 20 2 13.5 11.205 .074 .167 4.253 .089 .201 3.514 29 21 330 80 4180 7900 53 63 285 295 -3.486
17 -2 82 0 25 89 84 35 1 108 -8 -13 103 0 37 123 116 43 140 -10 130 124 .19 100 -50 1.598 1.306 8 1 13 0 4.68 .274 -7 -15 330 80 4330 7900 53 63 300 310
18 -6 77 0 48 91 83 46 6 113 -8 -12 109 0 57 135 121 122 146 -10 136 131 .69 100 -50 1.501 1.649 10 1 1 1 3.727 3.486 -2 -18 330 80 4480 7900 53 63 315 325
19 65 148 0 86 84 83 20 75 124 4 3 123 0 51 123 120 32 145 5 149 4 148 .21 80 0 -3.96 -4.169 .548 .597 67 55 25 9 18.75 15.563 .053 .046 4.197 .064 .056 .212 79 68 239 52 4620 7920 56 64 330 338 -3.96
20 49 137 0 94 90 88 23 63 173 59 51 165 0 74 118 114 35 137 71 208 61 199 .38 60 -100 .327 .785 .792 56 50 62 40 1.068 .886 .937 1.041 3.741 1.128 1.254 .762 122 100 156 32 4780 7890 54 60 347 353 .174

Total number of rows: 43008

Table truncated, full table size 8113 Kbytes.




Supplementary data files not provided

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