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Sample GSM84964 Query DataSets for GSM84964
Status Public on Nov 23, 2005
Title p239-s1225 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-s1225 PBMC (VS)
Organism Homo sapiens
Characteristics p239-s1225 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16816.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
1 971 1025 74 199 897 826 921 948 85 210 847 749 0 0 352 418 40 78 100 100 100 98 1723 1596 1.086 .921 .884 .878 .897 1.461 80 483 .921 .89 110 2080 8230 31 42 76 87 0 1114 216 898 1.001 1030 814 .999 .961 .001 -.057
2 1206 1310 74 201 1132 1109 1065 1117 100 211 991 916 0 0 629 761 73 79 99 97 98 95 2241 1907 1.021 .98 .924 .891 .917 1.638 120 463 1.078 .87 120 2240 8230 31 43 92 104 0 1424 218 1205 1.065 1214 996 .939 1.005 .091 .007
3 4728 2425 75 206 4653 2219 4746 2194 120 215 4671 1988 0 0 1764 1246 109 88 100 100 100 99 6872 6659 2.097 .477 .426 .447 .434 1.37 120 489 .508 .93 130 2400 8230 30 43 107 120 0 2636 224 2412 .518 2385 2161 1.929 .463 -.948 -1.112
4 3378 2930 74 210 3304 2720 2967 2486 172 240 2893 2276 0 0 1346 1613 230 127 99 100 99 99 6024 5169 1.215 .823 .787 .766 .771 1.366 120 409 .922 .93 120 2570 8230 31 43 125 137 0 3185 228 2957 .895 2702 2474 1.118 .855 -.16 -.226
5 15627 7619 76 212 15551 7407 15794 7016 172 250 15718 6804 0 0 6062 3905 234 157 100 100 100 100 22958 22522 2.1 .476 .433 .454 .438 1.323 120 491 .497 .95 130 2720 8230 30 43 139 152 0 8282 230 8051 .518 7626 7396 1.932 .471 -.95 -1.088
6 1925 2752 76 216 1849 2536 1955 2385 145 243 1879 2169 0 0 593 1274 179 151 100 100 100 100 4385 4048 .729 1.372 1.154 1.286 1.274 1.381 80 394 1.533 .92 110 2890 8220 30 41 157 168 0 2991 235 2757 1.491 2592 2358 .671 1.255 .576 .327
7 14518 3810 73 201 14445 3609 15066 3427 117 223 14993 3226 0 0 7133 2296 126 109 100 100 100 99 18054 18219 4.002 .25 .215 .231 .235 1.354 120 502 .261 .96 130 3030 8240 31 44 170 183 0 4141 218 3923 .272 3725 3507 3.682 .234 -1.881 -2.096
8 1411 2199 72 198 1339 2001 1283 1835 93 215 1211 1637 0 0 642 1202 67 97 100 99 99 99 3340 2848 .669 1.494 1.352 1.427 1.461 1.329 120 449 1.649 .95 120 3210 8230 31 43 189 201 0 2390 215 2175 1.624 1995 1779 .616 1.469 .7 .555
9 1801 2235 71 191 1730 2044 1832 2131 75 203 1761 1940 0 0 691 1088 24 78 100 99 100 99 3774 3701 .846 1.182 1.102 1.105 1.138 1.389 120 453 1.292 .94 120 3350 8220 30 42 203 215 0 2429 208 2222 1.284 2316 2109 .779 1.197 .361 .26
10 799 957 73 190 726 767 844 894 85 211 771 704 0 0 277 445 44 92 100 97 98 96 1493 1475 .947 1.056 .913 .992 1.029 1.571 120 457 1.208 .89 120 3520 8230 31 43 220 232 0 1040 207 834 1.148 972 765 .871 .992 .2 -.011
11 2059 15398 75 196 1984 15202 2170 14858 83 210 2095 14662 0 0 713 7724 40 93 100 100 100 100 17186 16757 .131 7.662 6.999 7.303 7.589 1.474 120 471 9.052 .91 130 3670 8230 30 43 234 247 0 16737 213 16524 8.329 16150 15937 .12 7.607 3.058 2.927
12 732 1661 73 197 659 1464 531 1416 76 204 458 1219 0 0 502 828 24 84 100 100 100 100 2123 1677 .45 2.222 2.662 2.475 2.9 1.796 120 415 2.364 .74 120 3830 8220 30 42 251 263 0 1805 214 1591 2.415 1539 1325 .414 2.893 1.272 1.533
13 897 1413 73 201 824 1212 912 1261 81 211 839 1060 0 0 387 683 44 100 100 99 95 97 2036 1899 .68 1.471 1.263 1.447 1.449 1.39 120 444 1.603 .94 130 3990 8220 29 42 266 279 0 1536 218 1317 1.599 1371 1152 .625 1.373 .677 .458
14 541 812 75 210 466 602 459 751 113 253 384 541 0 0 355 378 178 332 91 75 57 37 1068 925 .774 1.292 1.409 1.266 1.326 1.608 120 387 1.241 .88 120 4120 8220 30 42 280 292 0 883 228 654 1.404 816 588 .712 1.531 .49 .615
15 5695 2429 76 209 5619 2220 5825 2329 108 249 5749 2120 0 0 1480 1162 165 307 100 98 100 95 7839 7869 2.531 .395 .369 .349 .362 1.582 120 449 .421 .91 130 4280 8230 30 43 295 308 0 2640 227 2413 .429 2532 2304 2.329 .401 -1.219 -1.319
16 761 904 73 200 688 704 742 855 84 210 669 655 0 0 277 390 47 84 100 97 100 96 1392 1324 .977 1.023 .979 .945 .977 1.6 80 335 1.132 .91 100 4440 8220 31 41 313 323 0 983 217 765 1.112 929 712 .899 1.064 .153 .09
17 672 576 73 198 599 378 643 527 82 212 570 329 0 0 203 208 31 88 100 97 100 90 977 899 1.585 .631 .577 .58 .545 1.773 80 390 .678 .78 110 4600 8230 31 42 328 339 0 626 215 411 .686 573 358 1.458 .627 -.544 -.673
18 1133 3321 73 189 1060 3132 1168 3095 84 206 1095 2906 0 0 260 1195 34 86 100 100 100 100 4192 4001 .338 2.955 2.654 2.866 2.696 1.373 120 441 3.351 .91 120 4760 8240 32 44 344 356 0 3610 205 3404 3.212 3364 3159 .311 2.885 1.683 1.528
19 690 410 73 194 617 216 669 392 81 202 596 198 0 0 172 163 34 77 100 78 100 60 833 794 2.856 .35 .332 .281 .324 2.486 80 371 .4 .61 110 4920 8230 31 42 360 371 0 446 211 235 .381 426 215 2.628 .361 -1.394 -1.47
20 1656 2115 73 201 1583 1914 1704 1895 79 205 1631 1694 0 0 404 873 29 73 100 100 100 100 3497 3325 .827 1.209 1.039 1.122 1.034 1.554 120 428 1.38 .87 120 5070 8240 32 44 375 387 0 2299 218 2080 1.314 2060 1841 .761 1.129 .394 .175

Total number of rows: 37632

Table truncated, full table size 8350 Kbytes.




Supplementary data files not provided
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