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Sample GSM6311 Query DataSets for GSM6311
Status Public on Apr 15, 2004
Title AML 24
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 24
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=750640LaserPower=3.873.57
Lot batch = shdj078
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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 �m 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 �m 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 �m 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
1 157 278 0 111 126 121 30 164 383 202 176 357 0 195 208 181 126 248 277 525 241 489 .29 90 0 .755 .619 1.113 1.115 82 80 61 25 .812 .593 1.232 1.121 3.136 1.687 1.536 7.946 366 333 339 52 2600 8600 15 24 63 72 .755
2 1322 1447 0 674 127 125 28 1267 2508 2336 2531 2703 0 944 189 172 93 236 3200 3436 3467 3703 .96 90 0 1.337 1.391 2.105 1.863 100 100 100 100 .542 .396 1.844 1.915 1.652 2.526 2.623 1.754 3603 3853 329 52 2750 8610 16 25 78 87 1.337
3 320 439 0 479 120 119 24 561 719 557 506 668 0 443 171 162 65 222 763 985 693 915 .88 60 0 .444 1.115 1.026 1.088 100 96 93 81 1.007 .735 .993 1.581 2.249 1.36 2.166 .952 1118 826 171 32 2900 8620 19 25 95 101 .444
4 359 479 0 193 207 120 582 334 379 220 223 382 0 156 298 159 836 218 301 519 305 523 .64 70 0 -.148 -.233 .748 .69 15 0 0 0 1.518 1.108 .659 .621 2.79 .902 .851 .672 554 582 209 32 3040 8610 17 24 108 115 -.148
5 639 764 0 356 222 125 658 700 783 619 593 757 0 340 316 164 907 225 848 1073 812 1037 .91 90 0 .277 .346 .85 .864 46 5 19 0 1.131 .826 .884 .928 1.614 1.211 1.271 .894 1319 1232 353 52 3190 8620 17 26 122 131 .277
6 453 577 0 166 130 124 37 451 389 214 227 402 0 125 204 175 154 240 293 533 311 551 .53 70 0 -.621 -.543 .435 .496 100 100 65 18 2.107 1.538 .475 .501 2.049 .65 .686 .68 665 680 201 32 3330 8610 17 24 137 144 -.621
7 1038 1160 0 642 126 122 30 924 994 830 828 992 0 597 174 164 95 225 1137 1362 1134 1359 .93 80 0 .299 .128 .935 .859 92 90 92 82 1.113 .813 .898 .798 1.919 1.231 1.093 .916 1754 1866 250 52 3470 8620 18 26 151 159 .299
8 233 348 0 186 120 115 27 271 390 228 114 276 0 448 167 162 93 222 312 534 156 378 .18 80 0 .205 -.577 .587 .491 96 86 55 36 1.189 .868 .841 .489 4.719 1.153 .67 7.373 499 347 270 52 3610 8630 19 27 165 173 .205
9 242 360 0 141 120 118 29 257 566 409 381 538 0 204 164 157 78 215 560 775 522 737 .81 80 0 1.124 1.109 1.568 1.664 94 88 92 90 .628 .459 1.591 1.574 1.869 2.18 2.157 1.669 666 623 259 52 3780 8640 20 28 182 190 1.124
10 166 282 0 81 119 116 27 164 309 156 145 298 0 113 162 153 62 210 214 423 199 408 .54 70 0 .382 .259 .99 1.045 93 90 81 62 1.051 .767 .951 .873 2.34 1.303 1.197 1.913 320 311 192 32 3920 8630 19 26 196 203 .382
11 2281 2398 0 939 125 117 37 2102 654 485 466 635 0 205 179 169 79 232 664 896 638 870 .86 90 0 -1.662 -1.837 .238 .238 100 100 98 92 4.334 3.164 .231 .204 1.749 .316 .28 .21 2587 2747 351 52 4060 8630 18 27 209 218 -1.662
12 5533 5649 0 2142 123 116 33 5354 3705 3532 3636 3809 0 1651 193 173 119 237 4838 5075 4981 5218 .97 90 0 -.146 -.152 .626 .667 100 100 100 100 1.516 1.107 .66 .657 1.368 .904 .9 .663 8886 9169 326 52 4210 8630 18 27 224 233 -.146
13 713 831 0 340 122 118 30 714 694 538 534 690 0 248 183 156 125 214 737 951 732 945 .86 90 0 .046 .037 .764 .786 100 100 100 82 1.327 .969 .754 .749 1.576 1.032 1.026 .7 1252 1247 312 52 4350 8630 18 27 238 247 .046
14 245 365 0 99 124 120 34 237 610 457 454 607 0 166 165 153 76 210 626 836 622 832 .81 100 0 1.401 1.344 1.965 1.991 100 97 98 97 .519 .379 1.928 1.853 1.777 2.641 2.538 2.049 694 699 387 80 4510 8640 19 29 254 264 1.401
15 570 691 0 196 124 121 29 560 876 724 731 883 0 256 160 152 66 208 992 1200 1001 1210 .91 100 0 .825 .813 1.287 1.23 100 100 98 97 .773 .565 1.293 1.282 1.5 1.771 1.757 1.337 1284 1301 334 80 4650 8640 19 29 268 278 .825
16 2545 2666 0 992 122 121 33 2555 4059 3907 3723 3875 0 1121 160 152 71 208 5352 5560 5100 5308 .97 110 0 1.067 1.003 1.597 1.486 100 100 100 100 .654 .477 1.529 1.463 1.328 2.095 2.004 1.458 6462 6268 404 80 4800 8640 18 29 282 293 1.067
17 1039 1157 0 274 125 118 47 1082 6632 6471 6315 6476 0 1526 225 161 261 221 8864 9085 8651 8871 .97 110 0 3.034 3.058 5.994 5.99 100 100 100 100 .167 .122 5.981 6.078 1.203 8.193 8.326 6.086 7553 7354 382 80 4940 8640 18 29 296 307 3.034
18 7 122 0 73 124 115 43 24 189 20 1 170 0 98 234 169 270 232 27 259 1 233 .28 100 -50 -2.353 1.811 2.217 20 10 2 0 1.2 .876 .833 .143 3.178 1.142 .196 7.1 44 8 358 80 5090 8630 18 28 312 322 .191
19 2017 2137 0 702 123 120 31 1925 870 705 720 885 0 300 182 165 93 226 966 1192 986 1212 .9 90 0 -.995 -1.032 .352 .362 100 100 96 94 2.73 1.993 .366 .357 1.45 .502 .489 .345 2630 2737 264 52 5230 8640 19 28 326 335 -.995
20 926 1044 0 333 123 118 32 959 795 644 643 794 0 238 163 151 76 207 882 1089 881 1088 .92 110 0 -.12 -.072 .664 .652 100 100 100 98 1.489 1.087 .672 .694 1.426 .92 .951 .66 1603 1569 427 80 5380 8640 18 29 340 351 -.12

Total number of rows: 43008

Table truncated, full table size 9242 Kbytes.




Supplementary data files not provided
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