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Sample GSM6289 Query DataSets for GSM6289
Status Public on Apr 15, 2004
Title AML 70
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 70
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=700640LaserPower=3.964.6
Lot batch = shcz086
 
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
1 449 579 0 272 134 130 37 425 736 619 584 701 0 362 122 117 41 195 1032 1227 973 1168 .92 90 0 1.279 1.116 1.446 1.51 92 90 94 92 .687 .412 1.456 1.301 1.62 2.427 2.168 1.459 1044 1033 370 52 2000 7540 21 30 27 36 1.279
2 3104 3238 0 2092 137 134 40 3118 1619 1498 1349 1470 0 1019 126 121 43 202 2497 2698 2248 2450 .96 80 0 -.321 -.465 .495 .47 100 100 100 94 2.081 1.249 .48 .435 1.456 .801 .724 .468 4616 4453 256 52 2150 7550 23 31 43 51 -.321
3 2216 2352 0 789 141 136 50 2220 1159 1042 1036 1153 0 479 127 117 52 195 1737 1932 1727 1922 .95 70 0 -.354 -.36 .447 .477 100 100 100 100 2.131 1.278 .469 .468 1.422 .782 .779 .476 3262 3252 219 32 2290 7540 22 29 57 64 -.354
4 518 650 0 337 136 132 34 542 306 195 175 286 0 139 118 111 41 185 325 510 292 477 .9 80 0 -.738 -.829 .337 .347 92 90 88 78 2.779 1.668 .36 .338 1.92 .6 .563 .36 737 693 277 52 2440 7550 23 31 72 80 -.738
5 781 912 0 665 132 131 27 844 763 652 468 579 0 608 117 111 38 185 1087 1272 780 965 .93 80 0 .365 -.002 .703 .753 92 90 90 82 1.294 .777 .773 .599 1.865 1.288 .999 .831 1496 1249 234 52 2580 7550 23 31 86 94 .365
6 712 843 0 299 131 131 30 668 539 426 438 551 0 177 118 113 38 188 710 898 730 918 .92 70 0 .088 .036 .678 .637 100 96 100 96 1.568 .941 .638 .615 1.85 1.063 1.025 .608 1094 1150 220 32 2740 7550 23 30 102 109 .088
7 921 1051 0 588 135 130 56 867 1373 1261 1053 1165 0 944 117 112 39 187 2102 2288 1755 1942 .95 90 0 1.277 .93 1.353 1.361 94 90 96 96 .688 .413 1.454 1.143 1.811 2.424 1.906 1.527 2128 1974 320 52 2880 7550 22 31 115 124 1.277
8 723 857 0 270 143 134 66 700 336 218 206 324 0 141 122 118 41 197 363 560 343 540 .81 70 0 -.946 -1.074 .261 .272 100 100 87 84 3.211 1.927 .311 .285 1.992 .519 .475 .315 918 929 220 32 3020 7540 22 29 130 137 -.946
9 590 722 0 346 134 132 27 597 539 417 378 500 0 255 123 122 39 203 695 898 630 833 .87 70 0 .219 .095 .713 .824 96 96 93 93 1.432 .859 .698 .641 1.651 1.164 1.068 .681 1014 968 212 32 3180 7550 23 30 146 153 .219
10 503 633 0 210 130 130 30 474 266 151 134 249 0 97 119 115 41 192 252 443 223 415 .81 90 0 -.913 -1.171 .29 .332 96 94 86 71 3.139 1.883 .319 .266 1.704 .531 .444 .337 625 637 316 52 3320 7540 21 30 159 168 -.913
11 698 828 0 1194 130 130 28 1179 373 253 107 227 0 315 123 120 41 200 422 622 178 378 .94 80 0 -1.483 -1.969 .223 .222 94 90 69 57 4.66 2.796 .215 .153 2.183 .358 .255 .235 1432 805 266 52 3470 7550 23 31 175 183 -1.483
12 647 776 0 1646 130 129 28 1585 1330 1213 556 673 0 1329 119 117 40 195 2022 2217 927 1122 .99 80 0 .351 .518 .738 .771 100 96 98 96 1.307 .784 .765 .859 1.541 1.275 1.432 .791 2798 1203 257 52 3610 7550 23 31 189 197 .351
13 816 945 0 324 130 129 30 785 1156 1038 1044 1162 0 678 121 118 43 197 1730 1927 1740 1937 .91 70 0 1.14 1.092 1.048 1.342 100 100 93 93 .756 .454 1.322 1.279 2.124 2.204 2.132 1.545 1823 1860 212 32 3750 7540 22 29 203 210 1.14
14 389 524 0 182 133 135 28 349 394 278 308 424 0 142 118 116 40 193 463 657 513 707 .79 50 0 .409 .4 .789 .772 100 100 91 83 1.255 .753 .797 .792 1.806 1.328 1.32 .708 627 697 104 12 3890 7550 24 29 218 223 .409
15 507 640 0 224 137 133 49 448 11256 11137 12381 12500 0 5271 130 119 67 198 18562 18760 20635 20833 .94 90 0 5.373 5.347 25.817 25.696 94 92 100 100 .04 .024 24.859 24.42 1.425 41.432 40.7 25.407 11585 12888 352 52 4050 7540 21 30 232 241 5.373
16 5175 5306 0 2177 137 131 51 4464 6882 6761 7587 7708 0 3432 130 121 61 202 11268 11470 12645 12847 .99 90 0 1.336 1.289 1.539 1.544 100 100 100 100 .66 .396 1.515 1.466 1.527 2.524 2.443 1.528 11225 12762 329 52 4200 7540 21 30 247 256 1.336
17 653 778 0 481 127 125 26 680 6437 6322 5665 5780 0 3991 122 115 44 192 10537 10728 9442 9633 .96 100 0 3.954 3.854 10.12 9.686 93 91 100 100 .108 .065 9.297 8.675 1.541 15.495 14.459 9.229 7002 6318 393 80 4350 7550 22 32 262 272 3.954
18 492 618 0 702 130 126 31 671 719 603 168 284 0 1476 117 116 39 193 1005 1198 280 473 .91 70 -100 -.813 .424 .312 96 96 90 71 1.113 .668 .899 .341 3.287 1.498 .569 1.54 1274 660 210 32 4490 7540 22 29 277 284 .583
19 1638 1772 0 969 361 134 1459 1632 549 433 412 528 0 291 209 116 708 193 722 915 687 880 .89 70 0 -1.177 -1.254 .253 .256 53 12 15 0 3.769 2.261 .265 .252 1.559 .442 .419 .269 2065 2050 221 32 4650 7540 22 29 293 300 -1.177
20 1076 1218 0 534 451 142 1702 1078 627 511 562 678 0 287 247 116 827 193 852 1045 937 1130 .89 60 0 -.34 -.2 .435 .484 9 0 12 0 2.11 1.266 .474 .522 1.697 .79 .871 .568 1589 1638 161 32 4780 7540 23 29 307 313 -.34

Total number of rows: 43008

Table truncated, full table size 9398 Kbytes.




Supplementary data files not provided
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