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Sample GSM6331 Query DataSets for GSM6331
Status Public on Apr 15, 2004
Title AML 55
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 55
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=4.694.65
Lot batch = shdj098
 
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
1 384 507 0 310 125 123 32 419 1169 1042 1067 1194 0 615 132 127 41 159 1303 1461 1334 1493 .93 80 0 1.636 1.796 2.885 2.477 88 82 100 98 .402 .322 2.487 2.779 1.916 3.109 3.473 2.399 1461 1451 286 52 1620 8360 20 28 22 30 1.636
2 4080 4202 0 2793 124 122 28 4032 1443 1315 1201 1329 0 829 134 128 42 160 1644 1804 1501 1661 .96 90 0 -1.295 -1.442 .369 .314 100 100 100 100 3.066 2.453 .326 .294 1.875 .408 .368 .303 5347 5281 317 52 1770 8360 19 28 36 45 -1.295
3 1291 1412 0 1447 126 121 29 1597 1293 1159 785 919 0 997 135 134 37 168 1449 1616 981 1149 .96 60 0 -.141 -.396 .869 .705 90 87 100 96 1.378 1.102 .726 .608 3.082 .907 .76 .699 2756 2076 159 32 1910 8360 21 27 52 58 -.141
4 479 603 0 468 126 124 31 604 418 288 233 363 0 188 135 130 43 163 360 523 291 454 .9 80 0 -.747 -.718 .533 .486 100 100 100 88 2.097 1.678 .477 .486 1.994 .596 .608 .42 892 712 262 52 2050 8360 20 28 65 73 -.747
5 1102 1228 0 1032 127 126 31 1379 2674 2541 2196 2329 0 1716 136 133 41 166 3176 3343 2745 2911 .91 90 0 1.204 1.317 1.971 1.921 96 94 100 100 .543 .434 1.843 1.993 1.663 2.303 2.491 1.809 3920 3298 318 52 2210 8360 19 28 80 89 1.204
6 1117 1242 0 557 126 125 34 1139 788 652 674 810 0 274 144 136 50 170 815 985 843 1013 .89 60 0 -.483 -.407 .565 .59 100 100 96 96 1.747 1.398 .572 .603 1.908 .716 .754 .513 1791 1791 158 32 2340 8360 21 27 95 101 -.483
7 916 1041 0 1394 127 125 32 1368 2045 1911 1212 1346 0 1584 144 134 49 168 2389 2556 1515 1683 .96 80 0 .804 .726 1.944 1.564 94 94 100 100 .716 .573 1.397 1.323 2.085 1.746 1.654 1.256 3279 2128 253 52 2490 8370 21 29 109 117 .804
8 714 836 0 514 125 122 30 797 467 333 302 436 0 224 137 134 45 168 416 584 378 545 .86 80 0 -.937 -.919 .462 .442 94 92 92 84 2.393 1.915 .418 .423 2.584 .522 .529 .389 1130 1016 244 52 2630 8360 20 28 123 131 -.937
9 573 694 0 339 126 121 31 577 746 612 613 747 0 292 138 134 47 168 765 933 766 934 .92 100 0 .407 .419 1.182 1.04 98 93 98 97 .943 .754 1.061 1.07 1.757 1.326 1.337 1.009 1189 1186 378 80 2780 8360 19 29 137 147 .407
10 543 662 0 264 123 119 33 513 462 325 351 488 0 144 145 137 47 171 406 578 439 610 .81 60 0 -.337 -.308 .682 .636 100 93 96 90 1.578 1.263 .634 .646 2.154 .792 .808 .564 838 894 153 32 2920 8360 21 27 153 159 -.337
11 5338 5458 0 2434 125 120 32 5186 923 791 801 933 0 444 138 132 47 165 989 1154 1001 1166 .94 100 0 -2.391 -2.414 .139 .153 100 100 97 95 6.556 5.245 .153 .15 1.62 .191 .188 .15 5977 6139 367 80 3070 8360 19 29 166 176 -2.391
12 6255 6378 0 6065 126 123 30 8277 6393 6260 5014 5147 0 4257 137 133 44 166 7825 7991 6268 6434 .98 100 0 -.081 .003 .836 .745 100 100 100 100 1.322 1.058 .756 .802 1.492 .945 1.002 .728 14537 11269 338 80 3220 8360 19 29 181 191 -.081
13 982 1107 0 684 128 125 29 1155 2381 2248 1798 1931 0 1455 135 133 40 166 2810 2976 2248 2414 .94 100 0 1.283 1.195 1.895 1.97 98 98 100 100 .514 .411 1.946 1.831 1.565 2.433 2.289 2.084 3403 2780 325 80 3370 8360 19 29 196 206 1.283
14 525 651 0 219 129 126 31 539 743 608 595 730 0 227 139 135 41 169 760 929 744 913 .92 110 0 .496 .503 1.13 1.131 100 100 100 98 .887 .709 1.128 1.133 1.456 1.41 1.417 1.159 1147 1120 394 80 3500 8360 18 29 208 219 .496
15 914 1036 0 421 126 122 32 917 10593 10460 10554 10687 0 3793 138 133 43 166 13075 13241 13193 13359 .97 100 0 3.834 3.851 12.064 11.492 100 100 100 100 .088 .07 11.407 11.547 1.3 14.258 14.434 11.229 11377 11468 363 80 3660 8360 19 29 225 235 3.834
16 10037 10157 0 4467 126 120 41 10075 13050 12918 12469 12601 0 5335 145 132 65 165 16148 16313 15586 15751 .98 110 0 .681 .635 1.327 1.28 100 100 100 100 .78 .624 1.282 1.242 1.275 1.603 1.553 1.255 22993 22506 378 80 3810 8370 19 30 239 250 .681
17 2181 2299 0 1037 122 118 31 1885 44671 44541 51626 51756 10 20948 138 130 49 163 55676 55839 64533 64695 .98 120 0 4.884 4.887 25.097 23.223 97 95 100 100 .042 .034 23.629 23.671 1.41 29.536 29.588 23.06 46426 53807 419 120 3950 8360 18 30 253 265 4.884
18 23 142 0 171 121 119 29 69 195 63 28 160 0 112 137 132 45 165 79 244 35 200 .75 100 -50 .606 1.021 .999 45 22 40 26 1.095 .876 .913 1.217 3.021 1.141 1.522 .709 132 51 310 80 4090 8350 18 28 268 278 .191
19 4684 4806 0 1762 247 122 1136 4339 2474 2344 2461 2591 0 973 362 130 1934 163 2930 3093 3076 3239 .8 100 0 -.566 -.607 .55 .539 93 85 67 1 1.851 1.481 .54 .525 1.404 .675 .657 .996 6683 7145 314 80 4240 8360 19 29 283 293 -.566
20 2404 2527 0 723 221 123 1010 2345 1145 1014 1015 1146 0 360 317 131 1720 164 1268 1431 1269 1433 .75 110 0 -.888 -.922 .428 .428 93 72 2 0 2.313 1.85 .432 .422 1.322 .541 .528 1.345 3359 3419 398 80 4380 8360 18 29 296 307 -.888

Total number of rows: 43008

Table truncated, full table size 9459 Kbytes.




Supplementary data files not provided
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