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Sample GSM6253 Query DataSets for GSM6253
Status Public on Apr 15, 2004
Title AML 87
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 87
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=670630LaserPower=3.754.57
Lot batch = shco058
 
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 56 148 0 43 92 92 21 55 117 45 42 114 0 23 74 72 24 71 44 115 41 112 .25 50 0 -.318 -.444 .961 .873 75 58 83 33 1.222 1.247 .818 .75 3.319 .802 .735 .703 100 98 104 12 2010 7400 65 70 78 83 -.318
2 58 142 0 29 86 84 20 60 85 14 7 78 0 23 73 71 25 70 14 83 7 76 .28 60 0 -2.128 -3.079 .267 .282 90 71 25 9 4.286 4.371 .233 .121 3.942 .229 .118 .321 74 65 164 32 2160 7400 65 71 93 99 -2.128
3 322 409 0 158 88 87 21 344 130 59 53 124 0 52 74 71 23 70 58 127 52 122 .6 100 0 -2.572 -2.632 .164 .171 100 100 77 57 5.831 5.947 .172 .165 2.164 .168 .161 .148 403 375 324 80 2330 7390 62 72 108 118 -2.572
4 729 816 0 503 90 87 26 783 652 579 564 637 0 355 75 73 25 72 568 639 553 625 .96 90 0 -.464 -.399 .739 .729 100 100 100 98 1.352 1.379 .739 .774 1.506 .725 .758 .722 1362 1293 262 52 2460 7390 62 71 121 130 -.464
5 73 158 0 55 90 85 29 80 134 61 62 135 0 49 76 73 25 72 60 131 61 132 .44 60 0 -.42 -.264 .838 .912 84 59 75 53 1.311 1.338 .763 .849 2.333 .748 .833 .68 141 135 164 32 2610 7390 64 70 138 144 -.42
6 75 164 0 27 91 89 20 75 132 55 41 118 0 46 79 77 23 75 54 129 40 116 .51 50 0 -.476 -.9 .633 .795 100 91 66 41 1.364 1.391 .733 .547 2.728 .719 .536 .979 130 116 98 12 2740 7390 64 69 151 156 -.476
7 98 188 0 59 91 90 21 100 763 688 674 749 0 333 77 75 25 74 675 748 661 734 .86 80 0 2.754 2.753 6.821 6.803 90 80 100 100 .145 .148 6.88 6.878 1.49 6.745 6.743 7.067 788 772 274 52 2910 7400 64 72 167 175 2.754
8 748 839 0 451 94 91 23 768 1994 1921 1844 1917 0 1111 77 73 27 72 1883 1955 1808 1879 .95 80 0 1.294 1.273 2.439 2.568 100 100 100 100 .4 .408 2.501 2.465 1.489 2.452 2.417 2.57 2689 2592 232 52 3050 7390 63 71 181 189 1.294
9 139 228 0 93 92 89 22 135 1164 1086 1000 1078 0 576 81 78 33 76 1065 1141 980 1057 .89 90 0 2.979 2.818 9.57 8.266 86 76 100 100 .124 .127 8.044 7.194 1.788 7.887 7.053 7.871 1221 1139 326 52 3200 7400 63 72 195 204 2.979
10 69 157 0 44 91 88 19 75 120 53 48 115 0 30 71 67 23 66 52 118 47 113 .61 50 0 -.529 -.552 .652 .778 100 91 91 50 1.415 1.443 .707 .696 2.778 .693 .682 .63 128 117 104 12 3330 7400 65 70 210 215 -.529
11 323 414 0 112 92 91 22 343 207 135 136 208 0 72 76 72 26 71 132 203 133 204 .79 110 0 -1.374 -1.276 .353 .402 100 100 95 86 2.541 2.592 .394 .421 1.877 .386 .413 .381 478 459 496 80 3490 7390 61 72 223 234 -1.374
12 105 194 0 94 90 89 21 134 153 76 67 144 0 50 78 77 24 75 75 150 66 141 .7 60 -100 -.677 .541 .543 100 100 90 68 1.763 1.798 .567 .638 2.162 .556 .626 .528 210 172 156 32 3620 7390 64 70 239 245 -.847
13 110 198 0 62 90 88 22 112 126 48 42 120 0 43 79 78 26 76 47 124 41 118 .44 80 0 -1.251 -1.418 .474 .464 90 86 73 34 2.333 2.38 .429 .382 2.805 .42 .374 .388 160 152 294 52 3780 7390 63 71 254 262 -1.251
14 45 133 0 24 87 88 17 48 105 30 15 90 0 51 79 75 27 74 29 103 15 88 .19 50 0 -.707 -1.614 .5 .64 91 66 33 25 1.6 1.632 .625 .333 3.308 .613 .327 .93 78 60 104 12 3920 7390 64 69 269 274 -.707
15 757 843 0 438 87 86 21 840 507 433 378 452 0 242 79 74 27 73 425 497 371 443 .92 90 0 -.985 -1.03 .508 .537 100 100 100 100 1.94 1.979 .515 .499 1.398 .505 .49 .486 1273 1135 297 52 4080 7400 63 72 283 292 -.985
16 194 278 0 82 87 84 21 197 161 86 88 163 0 51 79 75 25 74 84 158 86 160 .72 80 0 -1.224 -1.169 .382 .453 96 94 86 78 2.291 2.337 .437 .454 2.287 .428 .445 .461 283 282 279 52 4220 7390 63 71 298 306 -1.224
17 65 158 0 59 92 93 20 74 130 55 57 132 0 31 79 75 27 74 54 127 56 129 .31 50 0 -.457 -.218 .734 .759 83 66 83 58 1.345 1.372 .743 .877 2.414 .729 .86 .505 129 122 104 12 4360 7390 64 69 313 318 -.457
18 71 160 0 31 91 89 25 66 98 25 16 89 0 34 76 73 23 72 25 96 16 87 .19 60 0 -1.429 -2.178 .349 .427 87 68 37 25 2.64 2.693 .379 .225 3.117 .371 .221 .348 91 87 147 32 4500 7400 65 71 327 333 -1.429
19 276 362 0 81 89 86 23 275 177 101 93 169 0 52 78 76 24 75 99 174 91 166 .76 100 0 -1.474 -1.598 .33 .349 100 100 96 87 2.723 2.777 .367 .337 1.886 .36 .33 .347 376 369 352 80 4660 7390 62 72 341 351 -1.474
20 34 121 0 40 90 87 23 35 88 11 9 86 0 31 80 77 24 75 11 86 9 84 .19 100 -50 -1.946 .56 .7 61 38 28 13 3.182 3.245 .314 .265 3.68 .308 .26 .489 46 43 325 80 4790 7380 61 71 354 364 -1.698

Total number of rows: 43008

Table truncated, full table size 8370 Kbytes.




Supplementary data files not provided
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