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Sample GSM84831 Query DataSets for GSM84831
Status Public on Nov 23, 2005
Title p239-s5961 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 p239-s5961 PBMC (VS)
Organism Homo sapiens
Characteristics p239-s5961 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16821.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
1 678 1287 109 297 569 990 720 1336 112 298 611 1039 0 0 218 400 21 63 97 96 95 95 1559 1650 .575 1.74 1.7 1.781 1.718 1.355 120 566 1.805 .96 120 1990 8740 38 50 96 108 0 847 195 651 1.145 879 684 .874 1.119 .195 .162
2 637 1436 111 304 526 1132 678 1556 115 312 567 1252 0 0 208 452 32 70 96 98 94 95 1658 1819 .465 2.152 2.208 2.226 2.134 1.336 120 397 2.204 .97 120 2150 8750 39 51 112 124 0 945 200 745 1.416 1024 824 .706 1.453 .502 .539
3 4770 3777 114 305 4656 3472 5306 4081 122 318 5192 3776 0 0 1660 1271 42 80 99 99 97 98 8128 8968 1.341 .746 .727 .775 .745 1.379 120 423 .742 .99 120 2310 8750 39 51 128 140 0 2485 201 2284 .491 2685 2484 2.038 .478 -1.027 -1.064
4 3368 4904 113 302 3255 4602 3415 5083 123 309 3302 4781 0 0 654 868 57 74 100 100 100 100 7857 8083 .707 1.414 1.448 1.419 1.409 1.112 80 396 1.391 .99 110 2470 8740 38 49 144 155 0 3226 199 3028 .93 3344 3145 1.075 .953 -.104 -.07
5 13751 10903 109 306 13642 10597 13159 10315 117 314 13050 10009 0 0 2792 2258 54 89 100 100 100 100 24239 23059 1.287 .777 .767 .775 .778 1.103 80 384 .761 .99 110 2620 8750 39 50 159 170 0 7173 201 6972 .511 6786 6585 1.957 .505 -.968 -.987
6 206 488 110 309 96 179 127 325 116 322 17 16 0 0 226 442 71 124 21 20 17 16 275 33 .536 1.865 .941 2.313 2.333 3.09 80 435 2.054 .88 110 2750 8740 38 49 172 183 -50 321 203 118 1.227 214 11 .815 .619 .295 -.692
7 15396 5573 113 309 15283 5264 17381 6326 119 318 17268 6017 0 0 6701 2184 70 113 100 100 100 100 20547 23285 2.903 .344 .348 .352 .334 1.216 120 466 .337 .99 120 2940 8740 38 50 191 203 0 3666 203 3463 .227 4162 3959 4.413 .229 -2.142 -2.125
8 126 303 111 297 15 6 117 279 114 301 6 -18 0 0 45 76 31 69 16 21 7 6 21 -12 2.5 .4 null 3.851 3.311 3.63 80 381 7.217 .22 110 3070 8740 38 49 204 215 -50 199 195 4 .263 184 null 3.8 null -1.926 null
9 1339 2861 111 284 1228 2577 1372 2901 114 289 1261 2617 0 0 283 533 29 66 100 100 100 100 3805 3878 .477 2.099 2.075 2.11 2.104 1.174 80 421 2.103 .98 110 3240 8750 39 50 221 232 0 1882 187 1695 1.381 1909 1722 .724 1.365 .465 .449
10 990 2001 112 297 878 1704 1023 1992 116 304 911 1695 0 0 184 357 24 67 100 100 100 100 2582 2606 .515 1.941 1.861 1.961 1.946 1.23 80 440 1.966 .97 110 3410 8740 38 49 238 249 0 1316 195 1121 1.277 1311 1115 .783 1.224 .353 .292
11 1448 22867 115 309 1333 22558 1594 24994 118 318 1479 24685 0 0 572 9624 27 76 97 100 97 100 23891 26164 .059 16.923 16.69 17.037 16.908 1.204 120 477 17.079 .99 120 3570 8740 38 50 254 266 0 15044 203 14841 11.133 16443 16240 .09 10.98 3.477 3.457
12 792 4020 114 308 678 3712 763 3861 117 317 649 3553 0 0 194 831 24 77 100 100 100 100 4390 4202 .183 5.475 5.475 5.566 5.59 1.222 80 375 5.529 .97 110 3730 8740 38 49 270 281 0 2645 203 2442 3.602 2540 2338 .278 3.602 1.849 1.849
13 737 1907 112 298 625 1609 733 1974 116 305 621 1676 0 0 302 690 28 66 97 98 95 98 2234 2297 .388 2.574 2.699 2.731 2.569 1.469 120 408 2.548 .97 120 3890 8740 38 50 286 298 0 1255 196 1059 1.694 1299 1103 .59 1.776 .76 .828
14 1116 3025 111 292 1005 2733 1216 3427 115 298 1105 3135 0 0 522 1422 28 66 95 98 94 96 3738 4240 .368 2.719 2.837 2.855 2.735 1.493 120 389 2.753 .99 120 4030 8740 38 50 300 312 0 1990 192 1798 1.789 2255 2063 .559 1.867 .839 .9
15 7497 3877 112 297 7385 3580 8083 4129 115 299 7971 3832 0 0 2266 1185 22 60 100 100 100 100 10965 11803 2.063 .485 .481 .496 .483 1.358 120 418 .484 .98 120 4190 8740 38 50 316 328 0 2551 195 2355 .319 2716 2521 3.136 .316 -1.649 -1.661
16 681 1148 111 306 570 842 693 1161 115 305 582 855 0 0 148 211 23 61 100 100 100 98 1412 1437 .677 1.477 1.469 1.483 1.476 1.221 80 371 1.523 .96 110 4350 8730 37 48 332 343 0 755 201 554 .972 764 563 1.029 .966 -.041 -.049
17 749 1003 115 307 634 696 803 1030 121 309 688 723 0 0 261 313 71 64 96 94 93 92 1330 1411 .911 1.098 1.051 1.032 1.058 1.5 120 404 1.139 .96 120 4500 8740 38 50 347 359 0 660 202 458 .722 678 476 1.385 .691 -.469 -.532
18 1726 7771 117 309 1609 7462 1900 8706 121 314 1783 8397 0 0 631 2880 33 71 98 100 98 100 9071 10180 .216 4.638 4.709 4.65 4.57 1.242 120 376 4.682 .99 120 4660 8740 38 50 363 375 0 5113 203 4909 3.051 5728 5524 .328 3.098 1.609 1.631
19 1048 1208 118 313 930 895 1094 1282 123 317 976 969 0 0 352 315 33 74 95 96 95 94 1825 1945 1.039 .962 .993 1.023 .957 1.662 120 353 .967 .97 120 4820 8740 38 50 379 391 0 795 206 589 .633 843 638 1.579 .653 -.659 -.614
20 2301 3887 115 304 2186 3583 2626 4234 118 307 2511 3930 0 0 838 1502 22 62 99 99 99 99 5769 6441 .61 1.639 1.565 1.608 1.61 1.154 120 408 1.674 .99 120 4970 8740 38 50 394 406 0 2557 200 2357 1.078 2786 2586 .927 1.03 .109 .042

Total number of rows: 37632

Table truncated, full table size 8551 Kbytes.




Supplementary data files not provided
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