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Sample GSM6273 Query DataSets for GSM6273
Status Public on Apr 15, 2004
Title AML 56
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 56
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=660630LaserPower=3.954.69
Lot batch = shcz213
 
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 GPL318
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
1 119 205 0 91 92 86 35 120 142 47 32 127 0 62 97 95 29 113 56 169 38 151 .65 60 0 -1.101 -1.643 .462 .479 81 59 50 31 2.553 2.145 .392 .269 2.87 .466 .32 .482 167 151 144 32 1940 8240 53 59 39 45 -1.101
2 280 360 0 561 83 80 22 538 293 193 130 230 0 167 101 100 26 119 230 349 155 274 .9 80 0 -1.227 -.855 .413 .365 100 96 94 88 2.788 2.342 .359 .464 1.815 .427 .553 .304 731 410 248 52 2070 8230 51 59 51 59 -1.227
3 45 129 0 70 87 84 22 67 119 16 17 120 0 33 106 103 32 123 19 142 20 143 .26 100 -50 -1.153 .651 .554 70 50 31 3 4.188 3.518 .239 .378 3.594 .284 .45 .246 83 62 393 80 2220 8220 49 59 65 75 -1.815
4 121 218 0 67 103 97 33 129 165 56 51 160 0 40 114 109 34 130 67 196 61 190 .29 70 0 -.952 -.995 .4 .446 90 84 71 28 2.304 1.935 .434 .421 2.613 .517 .502 .322 185 172 196 32 2380 8210 49 56 82 89 -.952
5 21 108 0 39 95 87 57 27 106 9 9 106 0 27 99 97 28 115 11 126 11 126 .05 100 -50 -.971 .67 .667 16 2 20 6 3 2.52 .333 .429 3.951 .397 .51 .629 36 30 378 80 2510 8220 49 59 94 104 -1.333
6 91 178 0 90 92 87 26 108 152 54 51 149 0 48 100 98 27 117 64 181 61 177 .46 60 -100 -.584 .582 .545 90 75 68 50 2 1.68 .5 .56 2.677 .595 .667 .349 162 142 172 32 2660 8240 53 59 111 117 -.748
7 50 135 0 51 88 85 23 61 147 45 33 135 0 57 103 102 30 121 54 175 39 161 .39 90 -100 -.348 .869 .685 78 51 51 30 1.356 1.139 .738 .66 3.368 .878 .786 1.053 106 83 368 52 2810 8220 49 58 124 133 -.187
8 116 201 0 53 90 85 27 124 116 15 8 109 0 30 103 101 30 120 18 138 10 130 .18 50 0 -2.796 -3.606 .137 .145 100 91 25 8 8.267 6.944 .121 .069 4.039 .144 .082 .187 139 124 104 12 2940 8220 51 56 139 144 -2.796
9 56 140 0 26 90 84 24 55 165 60 64 169 0 37 112 105 41 125 71 196 76 201 .49 50 0 .377 .444 .99 1.179 91 58 66 41 .917 .77 1.091 1.143 2.091 1.299 1.361 1.115 115 120 90 12 3090 8200 49 54 154 159 .377
10 84 169 0 40 87 85 20 79 134 32 26 128 0 41 107 102 35 121 38 160 31 152 .37 90 0 -1.052 -1.44 .315 .381 94 84 36 13 2.469 2.074 .405 .31 3.659 .482 .368 1.008 111 110 318 52 3240 8230 50 59 167 176 -1.052
11 67 156 0 34 97 89 30 64 145 47 39 137 0 52 106 98 37 117 56 173 46 163 .24 50 0 -.194 -.529 .768 .736 83 66 50 25 1.362 1.144 .734 .582 2.124 .874 .693 1.554 111 106 98 12 3370 8210 50 55 182 187 -.194
12 64 147 0 44 88 83 28 62 130 26 22 126 0 38 109 104 33 124 31 155 26 150 .37 70 0 -1.002 -1.289 .645 .667 81 53 46 15 2.385 2.003 .419 .344 2.33 .499 .409 .63 88 86 224 32 3530 8220 50 57 197 204 -1.002
13 25 107 0 35 85 82 20 29 116 12 11 115 0 36 108 104 32 124 14 138 13 137 .09 100 -50 -.933 .704 .868 57 33 17 6 2.417 2.03 .414 .44 3.71 .493 .524 3.86 41 36 392 80 3680 8220 49 59 211 221 -1.021
14 30 121 0 21 464 91 2505 27 269 152 125 242 0 155 176 117 348 139 181 320 149 288 .16 70 0 2.745 2.31 3.745 3.885 0 0 15 0 .178 .149 5.63 4.167 3.152 6.702 4.96 .079 179 155 190 32 3840 8220 50 57 228 235 2.745
15 89 179 0 87 389 90 2292 112 229 121 105 213 0 90 162 108 319 129 144 273 125 254 .74 80 0 .363 .49 1.146 1.112 0 0 7 0 .926 .778 1.08 1.18 1.864 1.286 1.404 1.063 233 194 228 52 3970 8220 50 58 241 249 .363
16 228 313 0 184 88 85 23 274 562 457 330 435 0 332 105 105 32 125 544 669 393 518 .9 110 0 .99 .785 1.701 1.533 97 96 100 98 .6 .504 1.668 1.447 1.631 1.986 1.723 1.796 731 558 403 80 4120 8220 48 59 254 265 .99
17 72 154 0 101 87 82 25 109 591 487 249 353 0 557 105 104 31 124 580 704 296 420 .55 90 0 2.411 2.042 3.557 3.66 86 69 96 92 .224 .188 4.468 3.458 2.627 5.319 4.117 5.364 596 321 313 52 4270 8210 48 57 270 279 2.411
18 25 107 0 72 85 82 21 46 106 3 -2 101 0 30 106 103 32 123 4 126 120 .14 100 -50 .6 .505 56 32 21 2 15.333 12.88 .065 4.169 .078 .171 49 23 383 80 4410 8210 48 58 284 294 -3.687
19 32 119 0 42 91 87 26 39 123 17 16 122 0 33 112 106 35 126 20 146 19 145 .06 70 0 -.946 -.748 .65 .809 50 31 25 9 2.294 1.927 .436 .5 3.873 .519 .595 .202 56 48 174 32 4570 8190 47 54 301 308 -.946
20 25 110 0 41 87 85 22 32 122 19 12 115 0 35 118 103 101 123 23 145 14 137 .05 100 -50 -.807 .723 .717 52 38 2 0 1.684 1.415 .594 .48 4.104 .707 .571 4.497 51 37 363 80 4700 8210 48 58 313 323 -.501

Total number of rows: 43008

Table truncated, full table size 8358 Kbytes.




Supplementary data files not provided

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