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Sample GSM6248 Query DataSets for GSM6248
Status Public on Apr 15, 2004
Title AML 49
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 49
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=690600LaserPower=3.654.52
Lot batch = shco049
 
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 9 104 0 29 97 95 25 16 96 12 6 90 0 34 88 84 31 101 14 116 7 108 .17 100 -50 -.316 1.198 1.028 27 12 26 8 1.333 1.107 .75 .667 3.715 .904 .803 5.082 28 15 425 80 1790 7870 74 84 46 56 -.146
2 22 112 0 28 93 90 20 25 103 19 12 96 0 37 88 84 32 101 23 124 14 116 .04 100 -50 -.606 1.23 1.434 50 23 32 12 1.316 1.092 .76 .545 4.906 .916 .657 16.385 44 34 354 80 1930 7870 74 84 60 70 -.127
3 316 405 0 202 91 89 19 324 102 19 10 93 0 36 86 83 31 100 23 123 12 112 .19 100 0 -3.823 -4.713 .127 .121 97 93 31 16 17.053 14.154 .059 .032 4.005 .071 .038 .035 343 326 323 80 2110 7880 75 85 78 88 -3.823
4 760 855 0 652 95 95 18 829 317 233 205 289 0 190 85 84 31 101 281 382 247 348 .83 80 0 -1.562 -1.622 .268 .268 100 100 92 78 3.558 2.953 .281 .27 2.039 .339 .325 .246 1062 965 181 52 2250 7880 76 84 93 101 -1.562
5 16 110 0 50 94 94 19 32 108 25 22 105 0 39 86 83 30 100 30 130 27 127 .18 100 -50 .728 .947 1.028 47 32 42 20 1.28 1.062 .781 1.375 4.542 .941 1.657 .952 57 38 372 80 2370 7860 73 83 104 114 -.087
6 34 127 0 25 91 93 18 37 104 25 19 98 0 38 88 79 36 95 30 125 23 118 .14 60 0 -.297 -.571 1.024 1.352 78 46 37 15 1.48 1.228 .676 .559 4.95 .814 .673 6.111 62 53 158 32 2530 7870 76 82 122 128 -.297
7 173 262 0 78 90 89 19 174 146 63 62 145 0 49 86 83 31 100 76 176 75 175 .59 80 0 -1.197 -1.212 .35 .421 96 94 75 48 2.762 2.292 .362 .358 2.076 .436 .432 .358 237 235 252 52 2680 7880 76 84 136 144 -1.197
8 988 1078 0 562 91 90 20 976 1202 1117 1059 1144 0 585 89 85 32 102 1346 1448 1276 1378 .89 80 0 .463 .369 1.315 1.166 100 96 100 100 .874 .725 1.144 1.072 2.575 1.379 1.291 1.102 2093 2047 230 52 2830 7880 76 84 151 159 .463
9 104 195 0 81 94 91 20 106 329 236 201 294 0 173 98 93 35 112 284 396 242 354 .72 80 -100 1.219 1.958 2.089 84 76 98 94 .449 .373 2.226 1.933 1.899 2.682 2.329 2.687 342 305 193 52 2980 7880 76 84 166 174 1.424
10 10 100 0 22 92 90 18 13 88 3 5 90 0 29 91 85 33 102 4 106 6 108 .13 100 -50 -.731 1.375 1.302 36 16 15 1 4.333 3.597 .231 .5 3.47 .278 .602 .148 16 15 368 80 3100 7860 73 83 177 187 -1.847
11 278 366 0 151 91 88 19 292 196 111 103 188 0 72 88 85 31 102 134 236 124 227 .63 100 0 -1.127 -1.164 .362 .403 97 96 87 70 2.631 2.183 .38 .371 2.369 .458 .446 .305 403 381 382 80 3270 7870 74 84 194 204 -1.127
12 79 169 0 32 98 90 35 82 157 69 57 145 0 45 94 88 32 106 83 189 69 175 .19 50 0 .02 -.202 .848 .878 100 58 75 50 1.188 .986 .841 .722 1.952 1.014 .869 .415 151 136 99 12 3400 7860 75 80 209 214 .02
13 101 193 0 41 98 92 28 102 123 30 25 118 0 33 97 93 35 112 36 148 30 142 .14 50 0 -1.497 -1.746 .273 .392 91 91 41 8 3.4 2.822 .294 .248 2.666 .354 .298 .141 132 126 104 12 3540 7860 75 80 223 228 -1.497
14 6 96 0 25 92 90 22 7 84 0 -2 82 0 30 89 84 33 101 0 101 99 .1 100 -50 1.168 .867 25 10 12 1 4.821 6.645 7 4 410 80 3680 7850 72 82 235 245
15 638 727 0 615 96 89 35 731 187 104 86 169 0 83 88 83 30 100 125 225 104 204 .68 90 0 -2.544 -2.622 .159 .15 96 92 82 59 7.029 5.834 .142 .135 2.738 .171 .162 .104 835 724 295 52 3840 7860 73 82 251 260 -2.544
16 188 281 0 101 97 93 35 205 120 36 39 123 0 42 89 84 32 101 43 145 47 148 .28 70 0 -2.241 -2 .286 .338 96 90 53 28 5.694 4.726 .176 .207 2.507 .212 .25 .112 241 227 182 32 3990 7850 73 80 267 274 -2.241
17 17 105 0 28 91 88 25 17 92 8 5 89 0 30 86 84 29 101 10 111 6 107 .04 100 -50 -1.497 1.349 1.5 28 7 26 5 2.125 1.764 .471 .294 4.05 .567 .354 13.839 25 22 325 80 4120 7840 71 81 279 289 -.819
18 7 100 0 28 95 93 21 10 94 9 8 93 0 38 89 85 34 102 11 113 10 112 .09 100 -50 .461 1.419 1.641 23 11 20 3 1.111 .922 .9 1.143 3.879 1.084 1.377 8.551 19 15 359 80 4270 7840 71 81 294 304 .117
19 190 280 0 90 92 90 18 207 158 74 60 144 0 55 89 84 33 101 89 190 72 173 .53 100 0 -1.215 -1.394 .328 .323 100 98 77 45 2.797 2.322 .357 .316 2.274 .431 .38 .3 281 250 330 80 4450 7850 72 82 312 322 -1.215
20 18 107 0 24 92 89 21 20 103 18 12 97 0 41 89 85 29 102 22 124 14 117 .15 100 -50 -.316 1.639 1.789 46 17 33 17 1.111 .922 .9 .667 4.304 1.084 .803 5.58 38 30 311 80 4560 7840 71 81 323 333 .117

Total number of rows: 43008

Table truncated, full table size 8026 Kbytes.




Supplementary data files not provided

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