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Sample GSM6320 Query DataSets for GSM6320
Status Public on Apr 15, 2004
Title AML 54
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 54
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=670650LaserPower=4.452.74
Lot batch = shdj087
 
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
1 448 554 0 252 109 106 29 466 1705 1602 1661 1764 0 822 107 103 34 106 1652 1758 1712 1819 .96 90 0 1.825 1.934 3.525 3.541 100 96 100 100 .291 .282 3.438 3.708 1.325 3.544 3.822 3.48 2068 2109 332 52 1740 8190 30 39 13 22 1.825
2 6121 6224 0 2074 105 103 26 5258 1340 1235 1300 1405 0 586 107 105 34 108 1273 1381 1340 1448 .97 90 0 -2.046 -2.191 .222 .241 100 100 100 100 4.257 4.13 .235 .212 1.376 .242 .219 .231 6493 7421 324 52 1890 8190 30 39 28 37 -2.046
3 1759 1860 0 852 105 101 30 1753 1064 962 918 1020 0 485 104 102 30 105 992 1097 946 1052 .97 60 0 -.822 -.894 .558 .543 100 100 100 100 1.822 1.768 .549 .522 1.32 .566 .538 .543 2715 2677 158 32 2040 8190 32 38 45 51 -.822
4 787 889 0 413 301 102 1436 783 660 555 561 666 0 291 260 105 999 108 572 680 578 687 .9 80 0 -.453 -.444 .703 .745 3 0 7 0 1.411 1.368 .709 .713 1.321 .731 .735 .593 1338 1348 254 52 2180 8190 31 39 58 66 -.453
5 1567 1670 0 665 259 103 1271 1537 2359 2256 2400 2503 0 989 225 103 885 106 2326 2432 2474 2580 .98 90 0 .598 .659 1.474 1.434 65 3 88 63 .681 .661 1.468 1.532 1.213 1.513 1.579 1.463 3793 3967 325 52 2330 8190 30 39 72 81 .598
6 1006 1106 0 398 105 100 30 987 1140 1038 1103 1205 0 455 107 102 36 105 1070 1175 1137 1242 .95 70 0 .117 .177 .99 1.027 100 100 100 100 .951 .922 1.052 1.096 1.472 1.084 1.13 1.051 2025 2109 215 32 2480 8180 30 37 88 95 .117
7 2009 2112 0 710 106 103 30 1884 3431 3325 3607 3713 0 1242 115 106 65 109 3428 3537 3719 3828 .98 70 0 .863 .888 1.775 1.724 100 100 100 100 .567 .55 1.765 1.795 1.171 1.819 1.851 1.764 5209 5616 222 32 2620 8180 30 37 102 109 .863
8 663 761 0 282 103 98 31 684 364 261 276 379 0 136 109 103 60 106 269 375 285 391 .9 80 0 -1.346 -1.22 .349 .357 100 100 92 80 2.621 2.542 .382 .416 1.702 .393 .429 .385 945 939 253 52 2770 8190 31 39 117 125 -1.346
9 505 603 0 186 101 98 26 504 339 235 227 331 0 101 107 104 34 107 242 349 234 341 .88 90 0 -1.057 -1.11 .46 .477 100 100 100 98 2.145 2.08 .466 .45 1.413 .481 .463 .438 739 732 325 52 2910 8180 29 38 130 139 -1.057
10 407 508 0 157 103 101 25 402 356 241 236 351 0 124 115 115 34 119 248 367 243 362 .83 60 0 -.694 -.742 .534 .565 100 100 93 93 1.668 1.618 .6 .58 2.005 .618 .598 .591 643 643 170 32 3060 8180 31 37 147 153 -.694
11 5529 5630 0 1900 105 101 29 5104 826 717 736 845 0 295 112 109 33 112 739 852 759 871 .96 90 0 -2.788 -2.865 .138 .141 100 100 100 98 7.119 6.905 .14 .133 1.225 .145 .137 .131 5821 6265 326 52 3220 8190 30 39 161 170 -2.788
12 8028 8130 0 4612 103 102 26 7974 11089 10980 10531 10640 0 6175 113 109 34 112 11320 11432 10857 10969 .99 100 0 .505 .435 1.416 1.381 100 100 100 100 .726 .704 1.377 1.312 1.272 1.42 1.352 1.362 18954 18559 331 80 3360 8190 30 40 175 185 .505
13 968 1070 0 584 104 102 25 1049 4187 4074 3739 3852 0 2586 116 113 36 116 4200 4316 3855 3971 .97 100 0 2.001 1.994 3.674 3.812 100 100 100 100 .257 .25 3.884 3.863 1.41 4.004 3.982 4.171 5123 4707 309 80 3500 8190 30 40 189 199 2.001
14 292 391 0 128 103 99 26 286 601 494 475 582 0 218 112 107 34 110 509 620 490 600 .92 120 0 .832 .746 1.801 1.712 99 95 100 100 .579 .562 1.727 1.627 1.533 1.781 1.677 1.807 780 767 450 120 3650 8190 29 41 203 215 .832
15 791 893 0 311 105 102 26 721 19244 19135 21858 21967 0 7165 113 109 34 112 19727 19839 22534 22646 .98 110 0 4.774 4.832 27.77 27.226 97 97 100 100 .038 .037 26.54 27.633 1.274 27.36 28.488 26.196 19856 22649 366 80 3790 8180 28 39 217 228 4.774
16 7091 7192 0 1777 105 101 25 6892 12857 12745 12697 12809 0 3229 115 112 38 115 13139 13255 13090 13205 .99 110 0 .931 .884 1.854 1.86 100 100 100 100 .541 .525 1.849 1.791 1.152 1.906 1.846 1.843 19637 19788 363 80 3930 8190 29 40 231 242 .931
17 1893 1992 0 662 101 99 24 1662 27495 27385 31015 31125 0 10162 113 110 39 113 28232 28345 31974 32088 .99 120 0 4.086 4.078 17.212 16.473 100 99 100 100 .061 .059 16.477 16.384 1.298 16.987 16.891 16.395 29047 32908 419 120 4080 8190 29 41 246 258 4.086
18 14 114 0 82 101 100 25 34 139 32 17 124 0 68 110 107 33 110 33 143 18 128 .52 100 -50 .324 1.087 1.286 33 20 35 20 1.063 1.031 .941 1.214 3.912 .97 1.252 .887 66 31 309 80 4220 8180 29 39 261 271 -.044
19 3546 3647 0 1158 103 101 27 3376 1457 1348 1443 1552 0 457 112 109 34 112 1390 1502 1488 1600 .98 110 0 -1.281 -1.253 .402 .405 100 100 100 100 2.504 2.429 .399 .407 1.247 .412 .42 .389 4724 4989 360 80 4370 8190 29 40 275 286 -1.281
20 2121 2222 0 433 104 101 27 2076 1939 1829 1865 1975 0 364 114 110 37 113 1886 1999 1923 2036 .98 110 0 -.139 -.142 .884 .886 100 100 100 100 1.135 1.101 .881 .879 1.175 .908 .906 .869 3905 3986 368 80 4520 8180 28 39 290 301 -.139

Total number of rows: 43008

Table truncated, full table size 9346 Kbytes.




Supplementary data files not provided
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