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Sample GSM84960 Query DataSets for GSM84960
Status Public on Nov 23, 2005
Title p378-s3194 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 p378-s3194 PBMC (VS)
Organism Homo sapiens
Characteristics p378-s3194 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16814.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
1 796 1113 85 234 711 879 758 936 87 265 673 702 0 0 332 752 20 316 100 84 100 57 1590 1375 .809 1.236 1.043 1.041 1.059 1.611 120 575 1.634 .88 120 1970 8590 39 51 69 81 0 870 183 687 .966 731 548 1.035 .815 -.05 -.295
2 820 1457 83 234 737 1223 776 1127 92 311 693 893 0 0 365 1969 64 668 94 66 94 22 1960 1586 .603 1.659 1.289 1.356 1.273 1.729 120 460 8.779 .76 120 2130 8580 38 50 85 97 -100 1138 183 955 1.296 880 698 .771 1.007 .375 .01
3 3962 3296 85 252 3877 3044 3847 2755 95 319 3762 2503 0 0 1518 2233 71 669 100 95 98 85 6921 6265 1.274 .785 .665 .702 .706 1.573 120 412 1.005 .83 120 2290 8590 39 51 101 113 0 2575 197 2378 .613 2152 1955 1.63 .52 -.705 -.944
4 2759 4274 85 242 2674 4032 2602 3669 89 253 2517 3427 0 0 1063 2462 31 101 100 100 100 100 6706 5944 .663 1.508 1.362 1.412 1.382 1.329 120 377 1.771 .92 120 2450 8590 39 51 117 129 0 3339 189 3150 1.178 2866 2677 .849 1.064 .236 .089
5 13619 13476 88 243 13531 13233 14494 12966 99 262 14406 12723 0 0 4317 6907 63 115 100 100 100 100 26764 27129 1.023 .978 .883 .913 .864 1.414 120 419 1.093 .92 120 2610 8590 39 51 133 145 0 10528 190 10338 .764 10130 9940 1.309 .69 -.388 -.535
6 1539 8211 90 266 1449 7945 1551 7797 103 292 1461 7531 0 0 262 2660 67 154 100 100 100 100 9394 8992 .182 5.483 5.155 5.318 5.252 1.399 80 400 6.185 .89 110 2760 8580 38 49 148 159 0 6415 208 6207 4.284 6091 5884 .233 4.027 2.099 2.01
7 12541 5643 88 255 12453 5388 13522 5350 98 274 13434 5095 0 0 5076 3051 59 141 100 100 100 100 17841 18529 2.311 .433 .379 .41 .406 1.361 120 462 .447 .93 120 2920 8590 39 51 164 176 0 4409 199 4209 .338 4180 3980 2.958 .296 -1.565 -1.755
8 1212 2931 86 252 1126 2679 1248 2858 91 256 1162 2606 0 0 339 1083 28 88 100 100 100 99 3805 3768 .42 2.379 2.243 2.28 2.259 1.302 120 461 2.582 .95 120 3080 8580 38 50 180 192 0 2290 197 2093 1.859 2233 2036 .538 1.752 .894 .809
9 1653 2798 87 252 1566 2546 1707 2586 90 257 1620 2334 0 0 355 1162 25 89 100 100 100 100 4112 3954 .615 1.626 1.441 1.521 1.478 1.391 80 408 1.812 .92 110 3230 8590 39 50 195 206 0 2186 197 1989 1.27 2020 1823 .787 1.126 .345 .171
10 923 1530 87 251 836 1279 884 1307 96 260 797 1056 0 0 204 756 40 93 100 100 100 100 2115 1853 .654 1.53 1.325 1.366 1.271 1.497 80 397 1.913 .87 110 3390 8590 39 50 211 222 0 1195 196 999 1.195 1021 825 .837 1.035 .257 .05
11 1671 22865 89 266 1582 22599 1651 23149 96 274 1562 22883 0 0 574 13418 39 98 100 100 100 100 24181 24445 .07 14.285 14.65 12.419 14.305 1.604 120 494 18.198 .88 120 3540 8580 38 50 226 238 0 17863 208 17655 11.16 18085 17877 .09 11.445 3.48 3.517
12 831 2622 88 260 743 2362 721 2205 92 272 633 1945 0 0 437 1695 25 102 100 100 100 100 3105 2578 .315 3.179 3.073 3.099 3.008 1.462 80 391 3.799 .83 110 3710 8580 38 49 243 254 0 2048 203 1845 2.484 1723 1520 .403 2.401 1.312 1.263
13 853 1554 88 266 765 1288 799 1464 90 278 711 1198 0 0 290 661 18 98 100 100 100 99 2053 1909 .594 1.684 1.685 1.528 1.612 1.585 120 468 1.935 .88 120 3850 8580 38 50 257 269 0 1214 208 1006 1.315 1144 936 .76 1.316 .395 .397
14 1447 2504 88 265 1359 2239 1379 2210 89 279 1291 1945 0 0 812 1477 21 109 100 100 100 98 3598 3236 .607 1.648 1.507 1.668 1.673 1.542 80 332 1.787 .91 100 4000 8590 40 50 273 283 0 1956 207 1749 1.287 1727 1520 .777 1.177 .364 .235
15 5159 3261 87 259 5072 3002 4760 2834 108 489 4673 2575 0 0 2239 2012 343 3131 100 33 100 7 8074 7248 1.69 .592 .551 .525 .524 1.476 120 496 .653 .93 120 4160 8590 39 51 288 300 0 2548 202 2345 .462 2214 2012 2.163 .43 -1.113 -1.216
16 937 1917 88 250 849 1667 977 1718 112 533 889 1468 0 0 316 947 375 3430 91 6 63 0 2516 2357 .509 1.963 1.651 1.834 1.681 1.44 80 413 8.57 .79 110 4330 8580 38 49 305 316 0 1498 195 1302 1.534 1342 1147 .652 1.29 .617 .367
17 614 681 85 251 529 430 601 634 90 265 516 383 0 0 176 244 26 118 100 96 100 82 959 899 1.23 .813 .742 .733 .759 1.72 80 337 .987 .76 100 4470 8590 40 50 320 330 0 532 196 336 .635 495 299 1.575 .58 -.655 -.786
18 992 5509 84 235 908 5274 1057 5365 90 248 973 5130 0 0 311 2065 33 100 99 100 96 100 6182 6103 .172 5.808 5.272 5.889 5.437 1.433 120 440 6.4 .92 120 4630 8600 40 52 335 347 0 4304 184 4120 4.538 4191 4008 .22 4.119 2.182 2.042
19 727 520 83 233 644 287 714 486 86 237 631 253 0 0 244 174 29 92 100 92 100 66 931 884 2.244 .446 .401 .391 .409 2.107 80 376 .408 .7 110 4790 8590 39 50 351 362 0 406 182 224 .348 380 198 2.872 .313 -1.522 -1.675
20 1505 3219 83 236 1422 2983 1582 3109 84 245 1499 2873 0 0 466 1201 18 88 100 99 99 99 4405 4372 .477 2.098 1.917 2.121 1.965 1.524 120 413 2.275 .93 120 4940 8600 40 52 366 378 0 2515 184 2330 1.639 2429 2245 .61 1.497 .713 .582

Total number of rows: 37632

Table truncated, full table size 8409 Kbytes.




Supplementary data files not provided
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