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Sample GSM84955 Query DataSets for GSM84955
Status Public on Nov 23, 2005
Title p878-s1562 PBMC (VS)
Sample type RNA
 
Channel 1
Source name CRF, 1 round of amplification, Addie's from 3/01 and Kate's from 7/00, combined
Organism Homo sapiens
Characteristics CRF, 1 round of amplification, Addie's from 3/01 and Kate's from 7/00, combined
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name p878-s1562 PBMC (VS)
Organism Homo sapiens
Characteristics p878-s1562 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16811.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 GPL3120
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 1719 2154 87 185 1632 1969 1790 2120 93 198 1703 1935 0 0 606 959 32 78 100 99 100 97 3601 3638 .829 1.206 1.136 1.132 1.128 1.47 120 551 1.29 .95 120 2370 8680 28 40 78 90 0 2393 206 2188 1.341 2356 2150 .746 1.262 .423 .336
2 1974 2532 94 218 1880 2314 2104 2538 102 235 2010 2320 0 0 746 1211 40 104 100 100 99 99 4194 4330 .812 1.231 1.154 1.182 1.187 1.475 120 375 1.345 .96 120 2520 8680 28 40 93 105 0 2813 242 2571 1.368 2820 2578 .731 1.282 .452 .359
3 12876 8623 99 239 12777 8384 13894 9781 183 277 13795 9542 0 0 3650 3196 281 153 100 100 100 99 21161 23337 1.524 .656 .692 .63 .682 1.318 120 373 .679 .97 120 2680 8680 28 40 109 121 0 9581 266 9316 .729 10868 10602 1.372 .769 -.456 -.38
4 6153 8598 96 233 6057 8365 6577 8831 256 294 6481 8598 0 0 1594 3415 814 314 99 100 96 100 14422 15079 .724 1.381 1.327 1.299 1.363 1.417 120 373 1.526 .94 120 2840 8680 28 40 125 137 0 9553 259 9294 1.534 9812 9553 .652 1.474 .618 .56
5 31281 25632 98 240 31183 25392 33585 29102 400 389 33487 28862 0 0 10078 11792 1267 567 100 100 99 100 56575 62349 1.228 .814 .862 .751 .824 1.312 120 424 .876 .97 130 3000 8680 27 40 140 153 -100 28480 267 28213 .905 32336 32069 1.105 .958 -.144 -.062
6 2938 4906 101 280 2837 4626 3149 4937 438 467 3048 4657 0 0 854 2349 1230 648 91 96 82 92 7463 7705 .613 1.631 1.528 1.484 1.475 1.682 80 368 1.954 .81 110 3130 8670 27 38 154 165 -100 5451 311 5140 1.812 5486 5174 .552 1.698 .857 .764
7 23832 7908 99 278 23733 7630 26126 8519 205 368 26027 8241 0 0 10618 4242 316 409 100 95 99 94 31363 34268 3.11 .321 .317 .296 .299 1.385 120 492 .328 .96 120 3310 8670 27 39 172 184 0 8787 309 8478 .357 9466 9157 2.799 .352 -1.485 -1.507
8 3758 9409 100 241 3658 9168 3799 9506 178 292 3699 9265 0 0 659 2243 218 230 100 100 100 100 12826 12964 .399 2.506 2.505 2.491 2.575 1.32 80 412 2.671 .95 110 3470 8670 27 38 188 199 0 10454 268 10187 2.785 10562 10294 .359 2.783 1.478 1.477
9 3085 5638 93 220 2992 5418 3131 5872 106 239 3038 5652 0 0 688 1816 55 111 100 100 100 100 8410 8690 .552 1.811 1.86 1.746 1.829 1.358 80 390 1.935 .95 100 3620 8670 28 38 204 214 0 6264 244 6020 2.012 6524 6280 .497 2.067 1.009 1.048
10 2102 2777 95 248 2007 2529 2114 2740 119 268 2019 2492 0 0 277 813 85 120 100 100 100 100 4536 4511 .794 1.26 1.234 1.207 1.201 1.339 80 446 1.315 .93 110 3780 8670 27 38 219 230 0 3086 276 2810 1.4 3044 2769 .714 1.371 .486 .456
11 2664 29125 95 241 2569 28884 2772 29909 111 261 2677 29668 0 0 1041 16356 57 126 100 100 100 100 31453 32345 .089 11.243 11.083 10.103 10.131 1.464 120 500 13.031 .94 120 3940 8670 27 39 235 247 0 32361 268 32093 12.493 33232 32964 .08 12.314 3.643 3.622
12 847 3954 97 257 750 3697 852 3796 122 283 755 3539 0 0 189 1226 85 132 98 100 98 100 4447 4294 .203 4.929 4.687 4.904 4.794 1.572 80 396 5.501 .89 110 4100 8670 27 38 251 262 0 4393 286 4108 5.477 4218 3932 .183 5.208 2.453 2.381
13 1990 3883 101 291 1889 3592 2057 4068 148 324 1956 3777 0 0 334 1192 112 151 100 100 100 100 5481 5733 .526 1.902 1.931 1.819 1.877 1.275 80 370 2.066 .95 110 4240 8680 28 39 265 276 0 4314 323 3991 2.113 4520 4197 .473 2.146 1.079 1.101
14 861 1907 97 270 764 1637 825 1806 127 302 728 1536 0 0 216 537 110 140 100 100 100 100 2401 2264 .467 2.143 2.11 2.102 2.024 1.37 80 371 2.29 .92 110 4380 8680 28 39 279 290 0 2119 300 1819 2.381 2007 1707 .42 2.344 1.251 1.229
15 9573 3595 96 245 9477 3350 10267 3603 132 264 10171 3358 0 0 3103 1631 147 108 100 100 100 100 12827 13529 2.829 .353 .33 .333 .337 1.492 120 440 .358 .92 120 4550 8680 28 40 296 308 0 3994 272 3722 .393 4003 3731 2.546 .367 -1.348 -1.447
16 1153 1377 94 233 1059 1144 1168 1313 131 250 1074 1080 0 0 254 384 143 106 100 100 100 100 2203 2154 .926 1.08 1.006 1.05 1.068 1.397 80 358 1.079 .9 110 4710 8670 27 38 312 323 0 1530 259 1271 1.2 1459 1200 .833 1.117 .263 .16
17 1284 850 90 205 1194 645 1330 820 107 218 1240 615 0 0 419 305 57 83 100 99 100 96 1839 1855 1.851 .54 .496 .51 .524 1.527 120 406 .547 .89 120 4860 8680 28 40 327 339 0 944 228 717 .6 911 683 1.666 .551 -.736 -.86
18 2242 8880 88 188 2154 8692 2306 8693 111 199 2218 8505 0 0 582 3766 78 76 100 100 98 100 10846 10723 .248 4.035 3.835 3.758 3.79 1.455 120 399 4.657 .93 120 5010 8680 28 40 342 354 0 9867 209 9658 4.484 9659 9450 .223 4.261 2.165 2.091
19 1098 532 85 187 1013 345 1099 490 103 195 1014 303 0 0 304 207 74 65 100 95 100 84 1358 1317 2.936 .341 .299 .297 .315 1.821 120 414 .344 .8 120 5170 8680 28 40 358 370 0 591 208 383 .378 544 337 2.643 .332 -1.402 -1.591
20 3298 3608 89 203 3209 3405 3517 3241 122 211 3428 3038 0 0 983 1764 95 83 98 98 98 98 6614 6466 .942 1.061 .886 1.008 .914 1.721 120 469 1.194 .91 120 5320 8680 28 40 373 385 0 4009 226 3783 1.179 3601 3376 .848 .985 .238 -.022

Total number of rows: 37632

Table truncated, full table size 8335 Kbytes.




Supplementary data files not provided
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