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Sample GSM6321 Query DataSets for GSM6321
Status Public on Apr 15, 2004
Title AML 59
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 59
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=740650LaserPower=4.424.39
Lot batch = shdj088
 
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 GPL319
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
1 641 762 0 253 124 121 30 645 937 745 786 978 0 298 195 192 72 267 1035 1301 1092 1358 .93 80 0 .682 .768 1.119 1.138 100 100 98 98 .866 .623 1.155 1.226 1.46 1.604 1.703 1.199 1390 1427 265 52 1820 8200 24 32 18 26 .682
2 5064 5185 0 3220 126 121 31 5182 993 807 756 942 0 555 190 186 67 258 1121 1379 1050 1308 .97 100 0 -2.209 -2.27 .146 .153 100 100 95 90 6.421 4.623 .156 .149 1.68 .216 .207 .158 5989 5820 358 80 1970 8200 23 33 32 42 -2.209
3 1809 1934 0 955 132 125 38 2078 2202 2020 1884 2066 0 802 189 182 74 253 2806 3058 2617 2869 .95 70 -100 .533 .999 .975 100 100 100 100 1.029 .741 .972 1.041 1.339 1.35 1.446 .957 4098 3693 186 32 2100 8200 24 31 46 53 .433
4 714 839 0 390 128 125 34 744 928 750 717 895 0 390 189 178 68 247 1042 1289 996 1243 .93 80 0 .486 .48 1.04 1.003 100 100 100 100 .992 .714 1.008 1.004 1.584 1.4 1.395 .996 1494 1431 271 52 2260 8200 24 32 62 70 .486
5 1271 1394 0 462 124 123 31 1319 1009 834 876 1051 0 333 184 175 62 243 1158 1401 1217 1460 .95 90 0 -.187 -.063 .621 .636 100 100 100 98 1.582 1.139 .632 .689 1.273 .878 .957 .634 2153 2147 307 52 2410 8200 23 32 76 85 -.187
6 1181 1308 0 453 132 127 47 1185 523 349 359 533 0 160 186 174 71 242 485 726 499 740 .85 70 0 -1.29 -1.244 .279 .296 100 100 96 90 3.395 2.445 .295 .304 1.526 .409 .422 .286 1534 1540 193 32 2540 8190 23 30 90 97 -1.29
7 2398 2519 0 1235 126 121 40 2299 3866 3695 3893 4064 0 2094 182 171 71 238 5132 5369 5407 5644 .97 90 0 1.158 1.173 1.578 1.609 100 98 100 100 .622 .448 1.607 1.623 1.345 2.232 2.255 1.643 5994 6291 313 52 2690 8200 23 32 104 113 1.158
8 1016 1131 0 303 117 115 28 960 511 349 365 527 0 146 173 162 60 225 485 710 507 732 .85 80 0 -.986 -1.003 .349 .372 100 100 100 96 2.751 1.981 .364 .359 1.498 .505 .499 .34 1309 1381 264 52 2840 8200 24 32 120 128 -.986
9 725 840 0 178 121 115 42 735 592 418 430 604 0 142 181 174 69 242 581 822 597 839 .85 90 0 -.34 -.28 .536 .57 100 100 96 96 1.758 1.266 .569 .593 1.717 .79 .824 .565 1153 1155 318 52 2980 8190 22 31 133 142 -.34
10 473 589 0 122 118 116 30 476 510 342 329 497 0 120 182 168 67 233 475 708 457 690 .84 70 0 -.003 -.05 .69 .634 100 100 100 96 1.392 1.002 .718 .696 1.538 .998 .966 .723 818 802 199 32 3130 8200 24 31 149 156 -.003
11 7320 7440 0 2415 123 120 31 6982 1082 913 923 1092 0 379 180 169 65 235 1268 1503 1282 1517 .96 100 0 -2.461 -2.514 .124 .13 100 100 100 96 7.647 5.506 .131 .126 1.361 .182 .175 .128 7895 8243 376 80 3270 8200 23 33 162 172 -2.461
12 12214 12335 0 4676 122 121 28 12195 6307 6136 6348 6519 0 2452 178 171 62 238 8522 8760 8817 9054 .99 100 0 -.517 -.47 .501 .494 100 100 100 100 1.987 1.431 .503 .52 1.17 .699 .722 .503 18331 18562 357 80 3420 8200 23 33 177 187 -.517
13 1476 1595 0 583 122 119 28 1470 2664 2495 2606 2775 0 1034 173 169 59 235 3465 3700 3619 3854 .97 100 0 1.237 1.294 1.681 1.659 100 100 100 100 .589 .424 1.697 1.766 1.3 2.357 2.452 1.732 3965 4082 339 80 3570 8200 23 33 192 202 1.237
14 490 611 0 149 124 121 31 525 1329 1155 1163 1337 0 313 176 174 63 242 1604 1846 1615 1857 .93 110 0 1.611 1.721 2.203 2.199 100 100 100 100 .455 .327 2.2 2.373 1.338 3.056 3.296 2.309 1680 1653 365 80 3710 8200 22 33 205 216 1.611
15 1065 1189 0 311 126 124 30 1046 10653 10481 10721 10893 0 3036 176 172 62 239 14557 14796 14890 15129 .98 110 0 3.799 3.805 9.994 10.192 100 100 100 100 .1 .072 10.02 10.067 1.192 13.917 13.981 10.141 11527 11786 374 80 3860 8200 22 33 220 231 3.799
16 10213 10334 0 2324 125 121 27 9776 9142 8967 9596 9771 0 2205 183 175 73 243 12454 12697 13328 13571 .98 110 0 .349 .384 .91 .937 100 100 100 100 1.09 .785 .917 .94 1.194 1.274 1.305 .916 18743 19809 389 80 4000 8200 22 33 234 245 .349
17 3146 3265 0 577 123 119 31 3075 15853 15676 16053 16230 0 2514 193 177 128 246 21772 22018 22296 22542 .99 110 0 2.824 2.825 5.133 5.106 100 100 100 100 .196 .141 5.098 5.103 1.135 7.08 7.087 5.133 18751 19199 373 80 4150 8190 21 32 249 260 2.824
18 12 130 0 194 121 118 31 74 248 69 25 204 0 163 190 179 131 249 96 344 35 283 .74 100 -50 1.533 1.502 1.4 36 27 18 7 1.072 .772 .932 2.083 2.935 1.295 2.894 .952 143 37 310 80 4290 8200 23 33 264 274 .373
19 4653 4772 0 1178 122 119 28 4575 4980 4815 4968 5133 0 1309 168 165 57 229 6688 6917 6900 7129 .99 110 0 .548 .568 1.046 1.06 100 100 100 100 .95 .684 1.052 1.068 1.158 1.462 1.483 1.055 9390 9621 349 80 4440 8200 22 33 278 289 .548
20 2930 3049 0 507 121 119 31 2878 1827 1661 1714 1880 0 436 172 166 58 231 2307 2538 2381 2611 .97 110 0 -.319 -.3 .563 .571 100 100 100 100 1.733 1.248 .577 .585 1.231 .802 .812 .585 4539 4644 374 80 4580 8200 22 33 292 303 -.319

Total number of rows: 43008

Table truncated, full table size 9397 Kbytes.




Supplementary data files not provided
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