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Sample GSM84899 Query DataSets for GSM84899
Status Public on Nov 23, 2005
Title s7853, p457, Pax
Sample type RNA
 
Channel 1
Source name Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Organism Homo sapiens
Characteristics Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name s7853, p457, Pax
Organism Homo sapiens
Characteristics s7853, p457, Pax
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25813.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 22, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3122
Series (1)
GSE3649 Individuality and variation in gene expression patterns in human blood.

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
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.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 3709 6313 389 276 3320 6037 3580 6375 398 282 3191 6099 0 0 698 998 81 81 100 100 100 100 9357 9290 .55 1.818 1.911 1.83 1.863 1.16 80 453 1.784 .98 110 2250 8930 26 37 34 45 0 5010 219 4791 1.443 5060 4840 .693 1.517 .529 .601
2 4008 10849 385 277 3623 10572 3958 10953 399 293 3573 10676 0 0 643 1830 82 114 100 100 100 100 14195 14249 .343 2.918 2.988 2.915 2.972 1.15 80 391 2.935 .98 110 2390 8920 25 36 48 59 0 8610 220 8390 2.316 8693 8473 .432 2.371 1.212 1.246
3 3517 8091 386 269 3131 7822 3170 8120 421 306 2784 7851 0 0 1040 1968 260 222 100 100 100 100 10953 10635 .4 2.498 2.82 2.537 2.63 1.202 80 446 2.494 .97 110 2550 8920 25 36 64 75 0 6421 213 6208 1.983 6444 6231 .504 2.238 .987 1.162
4 4976 10698 397 276 4579 10422 4868 10990 432 325 4471 10714 0 0 1283 2935 273 263 100 100 100 100 15001 15185 .439 2.276 2.396 2.262 2.38 1.241 80 447 2.31 .96 110 2720 8910 24 35 81 92 0 8490 219 8271 1.806 8722 8503 .554 1.902 .853 .927
5 2974 3476 387 266 2587 3210 2443 2977 397 288 2056 2711 0 0 1283 1480 90 139 100 100 100 100 5797 4767 .806 1.241 1.319 1.257 1.251 1.19 80 448 1.219 .98 110 2870 8910 24 35 96 107 0 2759 211 2548 .985 2363 2152 1.015 1.046 -.022 .066
6 3179 12797 378 266 2801 12531 3133 13390 384 275 2755 13124 0 0 458 2278 77 131 100 100 100 100 15332 15879 .224 4.474 4.764 4.439 4.607 1.202 80 436 4.574 .98 110 3040 8920 25 36 113 124 0 10156 211 9945 3.551 10627 10416 .282 3.781 1.828 1.919
7 5790 13479 374 267 5416 13212 5418 13506 386 295 5044 13239 0 0 1311 3112 100 192 100 100 100 100 18628 18283 .41 2.439 2.625 2.427 2.553 1.235 80 421 2.472 .97 110 3190 8920 25 36 128 139 0 10698 212 10486 1.936 10719 10507 .517 2.083 .953 1.059
8 3576 5155 387 265 3189 4890 3355 4811 396 288 2968 4546 0 0 904 1283 98 157 100 100 100 100 8079 7514 .652 1.533 1.532 1.541 1.546 1.159 80 422 1.521 .98 110 3350 8920 25 36 144 155 0 4091 210 3881 1.217 3818 3608 .822 1.216 .283 .282
9 2755 4253 384 263 2371 3990 2744 4334 400 290 2360 4071 0 0 506 928 118 182 100 100 100 100 6361 6431 .594 1.683 1.725 1.665 1.716 1.203 80 389 1.694 .97 110 3500 8920 25 36 159 170 0 3375 209 3167 1.336 3440 3231 .749 1.369 .417 .453
10 4595 7994 381 271 4214 7723 4689 8366 396 296 4308 8095 0 0 851 1846 120 188 100 100 100 100 11937 12403 .546 1.833 1.879 1.802 1.844 1.169 80 426 1.851 .98 110 3650 8920 25 36 174 185 0 6344 215 6129 1.455 6640 6425 .688 1.491 .541 .577
11 4423 7456 383 270 4040 7186 4003 6911 406 312 3620 6641 0 0 1392 2413 157 231 100 100 100 100 11226 10261 .562 1.779 1.835 1.777 1.825 1.172 80 448 1.789 .98 110 3820 8910 24 35 191 202 0 5917 214 5703 1.412 5485 5271 .708 1.456 .497 .542
12 3232 5375 377 257 2855 5118 3284 5505 387 289 2907 5248 0 0 449 1008 124 203 100 100 100 100 7973 8155 .558 1.793 1.805 1.774 1.803 1.13 80 365 1.788 .98 100 3970 8920 26 36 207 217 0 4266 204 4062 1.423 4369 4165 .703 1.433 .509 .519
13 3885 6281 379 258 3506 6023 3426 5707 379 272 3047 5449 0 0 1106 1852 75 84 100 100 100 100 9529 8496 .582 1.718 1.788 1.714 1.712 1.17 80 421 1.711 .98 110 4130 8920 25 36 222 233 0 4985 205 4780 1.363 4529 4325 .733 1.419 .447 .505
14 11056 14071 380 268 10676 13803 11361 15536 401 301 10981 15268 0 0 1949 3788 205 253 100 100 100 100 24479 26249 .773 1.293 1.39 1.249 1.318 1.212 80 396 1.315 .98 110 4290 8920 25 36 238 249 0 11167 213 10955 1.026 12330 12117 .975 1.103 .037 .142
15 4728 7375 379 267 4349 7108 4724 7463 402 298 4345 7196 0 0 733 1626 215 259 100 100 100 100 11457 11541 .612 1.634 1.656 1.612 1.626 1.127 80 327 1.654 .98 100 4440 8920 26 36 254 264 0 5853 212 5641 1.297 5923 5711 .771 1.314 .375 .394
16 4721 19842 382 263 4339 19579 5016 22230 387 275 4634 21967 0 0 1404 7561 81 89 100 100 100 100 23918 26601 .222 4.512 4.74 4.363 4.6 1.223 120 444 4.717 .98 120 4600 8920 25 37 269 281 0 15748 209 15539 3.581 17643 17434 .279 3.762 1.84 1.912
17 7680 5729 368 258 7312 5471 7815 5580 375 264 7447 5322 0 0 1484 1515 78 79 100 100 100 100 12783 12769 1.337 .748 .715 .736 .729 1.143 80 348 .76 .98 110 4750 8920 25 36 284 295 0 4547 205 4342 .594 4429 4224 1.684 .567 -.752 -.818
18 3457 3998 358 252 3099 3746 3540 3922 364 257 3182 3670 0 0 1219 1758 76 75 100 100 99 100 6845 6852 .827 1.209 1.153 1.187 1.163 1.214 120 490 1.257 .98 120 4900 8920 25 37 299 311 0 3173 200 2973 .959 3113 2913 1.042 .915 -.06 -.128
19 1875 1121 330 227 1545 894 1945 1145 341 232 1615 918 0 0 407 275 76 64 100 100 100 100 2439 2533 1.728 .579 .568 .571 .591 1.319 12 100 .573 .94 50 5070 8930 29 34 319 324 0 890 180 710 .459 909 729 2.178 .451 -1.123 -1.148
20 6059 5459 389 269 5670 5190 6080 5477 394 280 5691 5208 0 0 1632 1563 87 89 100 100 100 100 10860 10899 1.092 .915 .915 .91 .909 1.166 80 453 .917 .99 110 5200 8910 24 35 329 340 0 4333 213 4119 .726 4347 4133 1.377 .726 -.461 -.461

Total number of rows: 37632

Table truncated, full table size 8843 Kbytes.




Supplementary data files not provided
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