NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84938 Query DataSets for GSM84938
Status Public on Nov 23, 2005
Title p229-s3381 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 p229-s3381 PBMC (VS)
Organism Homo sapiens
Characteristics p229-s3381 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16804.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 1181 2669 98 195 1083 2474 1220 2753 102 206 1122 2558 0 0 447 975 29 86 100 100 100 98 3557 3680 .438 2.284 2.28 2.352 2.308 1.287 120 539 2.28 .98 120 2080 9060 39 51 53 65 0 2007 147 1860 1.718 2070 1923 .582 1.714 .78 .778
2 1211 3310 97 187 1114 3123 1239 3605 103 202 1142 3418 0 0 477 1464 33 94 98 98 98 98 4237 4560 .357 2.803 2.993 2.648 2.763 1.375 120 404 2.907 .98 120 2240 9050 38 50 69 81 0 2489 141 2348 2.108 2711 2570 .474 2.25 1.076 1.17
3 4957 6717 94 178 4863 6539 5238 6730 98 187 5144 6552 0 0 1394 2186 26 67 100 100 100 100 11402 11696 .744 1.345 1.274 1.337 1.288 1.232 120 470 1.38 .98 130 2400 9050 37 50 84 97 0 5050 134 4917 1.011 5060 4926 .989 .958 .016 -.062
4 3756 8949 97 182 3659 8767 3647 8429 100 191 3550 8247 0 0 1316 3685 25 70 100 100 100 100 12426 11797 .417 2.396 2.323 2.354 2.314 1.201 120 401 2.51 .98 120 2550 9050 38 50 100 112 0 6729 137 6592 1.802 6338 6201 .555 1.747 .849 .805
5 14781 22422 98 191 14683 22231 15353 22080 100 201 15255 21889 0 0 4619 8471 22 73 100 100 100 100 36914 37144 .66 1.514 1.435 1.497 1.481 1.268 120 394 1.568 .99 120 2710 9050 38 50 116 128 0 16859 144 16715 1.138 16602 16458 .878 1.079 .187 .109
6 1466 4151 93 184 1373 3967 1514 4317 97 196 1421 4133 0 0 487 1446 29 74 99 100 99 99 5340 5554 .346 2.889 2.909 2.952 2.869 1.343 120 391 2.94 .98 120 2870 9050 38 50 132 144 0 3121 138 2983 2.172 3246 3108 .46 2.187 1.119 1.129
7 12688 6405 92 179 12596 6226 12816 6593 95 193 12724 6414 0 0 5950 2855 28 85 100 100 100 100 18822 19138 2.023 .494 .504 .507 .498 1.226 120 388 .483 .98 120 3020 9050 38 50 147 159 0 4816 135 4681 .372 4957 4823 2.691 .379 -1.428 -1.4
8 1638 5447 89 178 1549 5269 1735 5917 93 189 1646 5739 0 0 527 1762 25 80 100 100 100 100 6818 7385 .294 3.402 3.487 3.412 3.335 1.233 120 421 3.45 .98 120 3180 9050 38 50 163 175 0 4095 134 3962 2.558 4449 4315 .391 2.622 1.355 1.39
9 2723 6570 92 182 2631 6388 2821 6782 94 187 2729 6600 0 0 641 1640 24 67 100 100 100 100 9019 9329 .412 2.428 2.418 2.415 2.406 1.143 80 380 2.416 .99 110 3330 9050 38 49 178 189 0 4940 137 4803 1.826 5099 4962 .548 1.818 .868 .863
10 1432 2831 94 182 1338 2649 1576 3078 97 192 1482 2896 0 0 391 923 25 69 100 100 100 100 3987 4378 .505 1.98 1.954 1.941 1.961 1.198 120 439 2.04 .98 120 3490 9050 38 50 194 206 0 2129 137 1992 1.489 2314 2177 .672 1.469 .574 .555
11 1585 17829 92 179 1493 17650 1738 19642 98 195 1646 19463 0 0 584 7282 42 87 99 100 98 100 19143 21109 .085 11.822 11.824 11.937 11.821 1.297 120 441 12.091 .99 120 3650 9050 38 50 210 222 0 13405 135 13271 8.889 14768 14634 .113 8.891 3.152 3.152
12 754 2478 90 179 664 2299 711 2430 98 193 621 2251 0 0 202 582 45 91 100 100 100 100 2963 2872 .289 3.462 3.625 3.503 3.46 1.242 80 425 3.497 .96 110 3800 9050 38 49 225 236 0 1863 135 1729 2.603 1827 1692 .384 2.725 1.38 1.446
13 1465 3554 87 186 1378 3368 1647 3893 91 197 1560 3707 0 0 513 1318 25 74 100 100 100 100 4746 5267 .409 2.444 2.376 2.442 2.391 1.229 120 488 2.488 .98 120 3960 9050 38 50 241 253 0 2672 140 2532 1.838 2927 2787 .544 1.787 .878 .837
14 682 1853 88 195 594 1658 643 1774 91 205 555 1579 0 0 263 582 23 72 100 100 100 100 2252 2134 .358 2.791 2.845 2.892 2.818 1.323 80 352 2.755 .95 100 4120 9050 39 49 258 268 0 1393 147 1247 2.099 1334 1187 .476 2.139 1.069 1.097
15 5239 3481 89 204 5150 3277 5923 3929 98 211 5834 3725 0 0 1881 1288 55 77 99 99 98 98 8427 9559 1.572 .636 .638 .637 .629 1.387 120 437 .641 .98 120 4280 9050 38 50 273 285 0 2617 153 2464 .478 2954 2801 2.09 .48 -1.064 -1.059
16 734 1390 89 198 645 1192 776 1422 98 208 687 1224 0 0 233 411 58 83 97 99 95 97 1837 1911 .541 1.848 1.782 1.913 1.882 1.457 120 400 1.878 .96 120 4430 9050 38 50 288 300 0 1045 149 896 1.39 1069 920 .72 1.34 .475 .422
17 578 785 89 190 489 595 597 817 95 208 508 627 0 0 185 236 35 104 96 95 96 91 1084 1135 .822 1.217 1.234 1.235 1.207 1.477 120 411 1.253 .92 120 4590 9050 38 50 304 316 0 590 143 447 .915 614 471 1.093 .928 -.128 -.108
18 1301 8753 92 188 1209 8565 1296 8615 102 202 1204 8427 0 0 346 2639 58 87 100 100 100 100 9774 9631 .141 7.084 6.999 7.067 6.932 1.207 120 425 7.284 .98 120 4750 9050 38 50 320 332 0 6581 141 6440 5.327 6477 6336 .188 5.263 2.413 2.396
19 1031 1059 94 184 937 875 1038 1143 118 203 944 959 0 0 324 356 107 99 100 96 100 94 1812 1903 1.071 .934 1.016 .847 .96 1.623 52 295 .869 .93 90 4890 9060 40 49 335 344 0 796 138 658 .702 859 721 1.424 .764 -.51 -.389
20 1856 3543 94 195 1762 3348 2015 3466 143 283 1921 3271 0 0 1083 2424 215 393 91 95 87 85 5110 5192 .526 1.9 1.703 1.845 1.847 1.551 80 356 2.072 .95 100 5080 9070 41 51 354 364 0 2664 147 2517 1.429 2606 2459 .7 1.28 .515 .356

Total number of rows: 37632

Table truncated, full table size 8523 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap