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Sample GSM6242 Query DataSets for GSM6242
Status Public on Apr 15, 2004
Title AML 48
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 48
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=690620LaserPower=3.324.48
Lot batch = shco038
 
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 10 106 0 68 98 96 25 21 124 3 -8 113 0 66 125 121 39 198 5 203 185 .18 100 -50 .803 .716 36 20 20 5 7 4.27 .143 3.943 .234 1.996 24 2 395 80 1920 7850 76 86 59 69 -2.094
2 29 122 0 53 121 93 167 33 116 -2 -3 115 0 48 133 118 149 193 -3 190 189 .03 100 -50 .803 1.035 1 0 1 0 4.103 .049 31 26 428 80 2070 7840 75 85 74 84
3 151 248 0 90 155 97 246 141 118 -6 -2 122 0 36 153 124 219 203 -10 193 200 .88 70 0 .225 .273 9 0 0 0 3.697 .601 135 149 191 32 2230 7850 77 84 91 98
4 449 537 0 641 93 88 40 551 381 264 228 345 0 218 121 117 63 192 433 625 374 566 .68 80 0 -.348 -.265 .543 .468 80 76 80 67 2.087 1.273 .479 .508 2.361 .785 .832 .329 815 677 256 52 2360 7860 78 86 104 112 -.348
5 111 203 0 147 106 92 49 144 215 101 64 178 0 122 117 114 39 187 166 352 105 292 .74 50 0 .201 -.081 .655 .748 75 66 66 41 1.426 .87 .701 .577 2.484 1.15 .945 .664 245 175 86 12 2530 7840 77 82 122 127 .201
6 3 91 0 29 90 88 26 3 125 10 -6 109 0 61 118 115 38 189 16 205 179 .3 100 -50 1.804 1.999 23 6 32 18 .3 .183 3.333 4.279 5.464 5.424 13 -3 353 80 2650 7840 75 85 132 142 2.45
7 -1 90 0 36 266 91 2334 -1 359 247 134 246 0 298 135 112 229 184 405 589 220 403 .72 90 0 6.202 9.33 0 0 38 19 4.203 .091 246 133 276 52 2790 7850 76 85 146 155
8 302 390 0 493 287 88 2487 445 427 316 244 355 0 363 138 111 244 182 518 700 400 582 .93 80 0 .219 .405 .914 .791 0 0 50 23 1.408 .859 .71 .808 2.146 1.164 1.325 .194 761 546 243 52 2940 7850 77 85 162 170 .219
9 76 166 0 99 91 90 23 88 633 516 423 540 0 417 121 117 41 192 846 1038 693 885 .74 100 0 3.265 3.19 4.771 4.606 72 63 90 88 .171 .104 5.864 5.566 2.156 9.613 9.124 6.157 604 499 331 80 3090 7850 76 86 176 186 3.265
10 -1 88 0 30 90 89 22 0 115 1 -7 107 0 50 118 114 40 187 2 189 175 .18 100 -50 1.581 1.543 18 10 22 8 3.181 7.728 1 -8 313 80 3240 7840 75 85 191 201
11 214 300 0 207 88 86 20 215 146 34 16 128 0 92 113 112 37 184 56 239 26 210 .09 110 0 -1.948 -3.028 .315 .22 80 73 38 21 6.324 3.857 .158 .075 3.967 .259 .123 18.429 249 230 327 80 3370 7850 75 86 203 214 -1.948
12 25 106 0 75 84 81 21 52 122 12 0 110 0 60 113 110 35 180 20 200 0 180 .46 100 -50 .89 .875 51 40 31 17 4.333 2.643 .231 3.975 .378 .732 64 25 317 80 3530 7840 75 85 220 230 -1.402
13 29 110 0 66 83 81 20 45 110 4 1 107 0 44 111 106 38 174 7 180 2 175 .14 100 -50 -4.145 .753 .749 55 45 17 8 11.25 6.863 .089 .034 3.932 .146 .057 .318 49 30 303 80 3680 7840 75 85 235 245 -2.779
14 -1 84 0 29 107 85 109 -2 103 -5 -7 101 0 42 113 108 41 177 -8 169 166 .23 100 -50 1.196 1.162 0 0 13 3 3.719 .163 -7 -8 329 80 3820 7840 75 85 249 259
15 395 478 0 395 115 83 130 375 144 36 24 132 0 75 115 108 44 177 59 236 39 216 .45 90 0 -2.668 -3.328 .258 .216 63 61 36 25 10.417 6.354 .096 .061 5.076 .157 .1 .094 411 419 258 52 3980 7860 77 86 265 274 -2.668
16 108 189 0 112 85 81 26 99 138 27 27 138 0 64 112 111 35 182 44 226 44 226 .44 80 0 -1.161 -1.287 .475 .387 63 57 40 21 3.667 2.237 .273 .25 3.445 .447 .41 .362 126 135 209 52 4120 7850 77 85 280 288 -1.161
17 5 88 0 59 85 83 20 10 103 -6 -22 87 0 51 112 109 36 179 -10 169 143 .14 100 -50 2.074 2 26 13 22 7 3.396 2.279 4 -17 312 80 4260 7840 75 85 293 303
18 -5 79 0 30 85 84 21 -2 106 4 0 102 0 42 109 102 37 167 7 174 0 167 .1 100 -50 1.289 1.292 23 10 21 6 3.645 6.299 2 -5 308 80 4410 7840 75 85 308 318
19 131 217 0 112 88 86 21 147 132 22 21 131 0 55 113 110 38 180 36 216 34 215 .25 110 0 -2.027 -1.928 .26 .246 85 80 33 15 6.682 4.076 .15 .16 3.861 .245 .263 .128 169 152 367 80 4550 7840 74 85 321 332 -2.027
20 96 183 0 106 96 87 51 107 217 104 111 224 0 109 117 113 39 185 170 356 182 367 .53 110 0 .672 .923 1.266 1.093 68 48 68 58 1.029 .628 .972 1.156 3.285 1.593 1.895 1.027 211 207 403 80 4680 7840 74 85 334 345 .672

Total number of rows: 43008

Table truncated, full table size 8221 Kbytes.




Supplementary data files not provided
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