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Sample GSM6268 Query DataSets for GSM6268
Status Public on Apr 15, 2004
Title AML 108
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 108
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=650650LaserPower=3.534.52
Lot batch = shcz077
 
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
1 273 434 0 140 164 161 38 277 964 866 859 957 0 395 102 98 30 104 921 1026 914 1018 .89 90 0 1.734 1.743 3.307 3.079 96 92 100 100 .32 .301 3.126 3.147 1.684 3.326 3.347 3.174 1143 1132 353 52 1900 8170 24 33 29 38 1.734
2 5787 5945 0 2814 162 158 36 5338 469 372 389 486 0 221 100 97 29 103 396 499 414 517 .94 80 0 -3.754 -3.806 .07 .068 100 100 98 96 14.349 13.488 .07 .067 1.454 .074 .072 .069 5710 6176 238 52 2040 8180 26 34 44 52 -3.754
3 1938 2093 0 1146 182 155 168 2014 1149 1049 1082 1182 0 523 103 100 31 106 1116 1222 1151 1257 .97 80 0 -.852 -.752 .559 .534 100 94 100 100 1.92 1.805 .521 .558 1.354 .554 .594 .49 3063 3020 242 52 2190 8180 26 34 59 67 -.852
4 609 768 0 418 188 159 280 657 860 759 800 901 0 421 106 101 36 107 807 915 851 959 .92 80 0 .297 .483 1.233 1.199 75 51 100 100 .866 .814 1.155 1.314 1.512 1.229 1.397 1.081 1416 1409 256 52 2330 8180 26 34 73 81 .297
5 486 646 0 304 161 160 38 456 264 163 180 281 0 109 112 101 61 107 173 281 191 299 .78 100 0 -1.395 -1.344 .36 .367 93 88 78 57 2.798 2.63 .357 .37 1.823 .38 .394 .325 619 666 351 80 2480 8180 25 35 87 97 -1.395
6 603 765 0 291 169 162 47 580 1459 1352 1423 1530 0 649 122 107 70 114 1438 1552 1514 1628 .94 80 0 1.31 1.328 2.337 2.308 100 98 98 98 .429 .403 2.331 2.36 1.398 2.48 2.51 2.403 1932 2026 267 52 2620 8180 26 34 102 110 1.31
7 935 1098 0 377 171 163 53 895 1445 1339 1337 1443 0 382 119 106 52 113 1424 1537 1422 1535 .93 70 0 .67 .605 1.626 1.588 100 96 100 100 .668 .628 1.496 1.43 1.517 1.592 1.521 1.456 2234 2272 218 32 2760 8170 25 32 116 123 .67
8 497 664 0 247 170 167 36 511 167 67 72 172 0 33 103 100 29 106 71 178 77 183 .57 60 0 -2.842 -2.698 .138 .131 96 93 87 65 7.627 7.169 .131 .145 2.045 .139 .154 .09 578 569 165 32 2910 8180 27 33 132 138 -2.842
9 144 304 0 83 160 160 36 158 320 217 229 332 0 81 105 103 32 110 231 340 244 353 .82 70 0 .547 .759 1.496 1.363 96 87 100 96 .728 .684 1.373 1.59 1.898 1.461 1.692 1.261 375 373 225 32 3060 8180 26 33 146 153 .547
10 373 528 0 183 156 155 36 363 126 29 26 123 0 37 100 97 28 103 31 134 28 131 .32 90 0 -3.557 -3.753 .1 .108 96 96 46 26 12.517 11.766 .08 .07 2.798 .085 .074 .057 392 399 348 52 3210 8180 25 34 160 169 -3.557
11 1693 1850 0 586 163 157 41 1387 213 114 119 218 0 61 107 99 45 105 121 227 127 232 .8 60 0 -3.516 -3.741 .078 .084 100 96 81 71 12.167 11.437 .082 .07 2.363 .087 .075 .074 1501 1812 170 32 3360 8180 27 33 177 183 -3.516
12 2196 2354 0 1463 163 158 39 2106 1334 1232 1297 1399 0 795 112 102 49 109 1311 1419 1380 1488 .98 80 0 -.684 -.67 .629 .591 100 100 100 96 1.709 1.607 .585 .591 1.462 .622 .628 .56 3338 3493 266 52 3500 8180 26 34 190 198 -.684
13 668 825 0 402 160 157 36 661 387 289 285 383 0 186 102 98 30 104 307 412 303 407 .92 80 0 -1.104 -1.14 .442 .437 96 94 94 88 2.287 2.15 .437 .427 1.615 .465 .454 .42 950 953 249 52 3640 8180 26 34 204 212 -1.104
14 42 198 0 55 160 156 36 50 129 31 22 120 0 40 100 98 29 104 33 137 23 128 .22 100 -50 -.844 .625 .606 51 35 40 17 1.613 1.516 .62 .524 3.095 .66 .557 .304 81 64 349 80 3790 8170 24 34 218 228 -.6
15 385 546 0 277 164 161 36 417 1040 939 803 904 0 575 105 101 30 107 999 1106 854 962 .95 100 0 1.26 1.15 2.265 2.251 93 92 100 100 .444 .417 2.252 2.086 1.427 2.396 2.219 2.245 1356 1188 345 80 3940 8180 25 35 233 243 1.26
16 4790 4953 0 2153 164 163 36 4363 5492 5390 5839 5941 0 2442 108 102 32 109 5734 5843 6212 6320 .98 90 0 .394 .375 1.35 1.26 100 100 100 100 .809 .761 1.235 1.219 1.453 1.314 1.297 1.208 9753 10629 316 52 4080 8180 25 34 247 256 .394
17 928 1090 0 570 164 162 37 863 4578 4474 4699 4803 0 2433 108 104 34 111 4760 4870 4999 5110 .96 100 0 2.463 2.429 5.833 5.305 95 91 100 100 .193 .181 5.184 5.064 1.664 5.515 5.387 5.034 5337 5627 372 80 4240 8180 25 35 263 273 2.463
18 36 201 0 98 168 165 39 71 122 11 4 115 0 32 114 111 43 118 12 130 4 122 .24 100 -50 -3.081 .463 .356 50 40 15 2 6.455 6.067 .155 .111 5.525 .165 .118 .148 82 40 367 80 4380 8170 24 34 277 287 -2.601
19 554 718 0 444 166 164 33 623 404 294 266 376 0 210 113 110 43 117 313 430 283 400 .92 90 0 -.994 -.969 .463 .48 96 96 92 82 2.119 1.992 .472 .48 2.115 .502 .511 .454 917 820 289 52 4530 8180 25 34 292 301 -.994
20 662 832 0 381 184 170 72 619 675 560 549 664 0 315 153 115 212 122 596 718 584 706 .92 80 0 -.055 -.181 .973 .914 88 86 82 65 1.105 1.039 .905 .829 1.846 .962 .882 .928 1179 1211 244 52 4670 8180 26 34 307 315 -.055

Total number of rows: 43008

Table truncated, full table size 9184 Kbytes.




Supplementary data files not provided
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