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Sample GSM84942 Query DataSets for GSM84942
Status Public on Nov 23, 2005
Title p085-s4194 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 p085-s4194 PBMC (VS)
Organism Homo sapiens
Characteristics p085-s4194 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16806.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
1 750 1030 88 197 662 833 802 1061 91 208 714 864 0 0 255 330 23 97 99 97 99 93 1495 1578 .795 1.258 1.21 1.263 1.241 1.433 120 591 1.281 .96 120 2330 8990 64 76 70 82 0 1132 216 915 1.383 1166 949 .723 1.33 .468 .411
2 1016 1458 88 196 928 1262 1033 1451 94 205 945 1255 0 0 193 305 27 78 100 100 100 100 2190 2200 .735 1.36 1.328 1.355 1.325 1.231 80 390 1.504 .9 110 2490 8990 64 75 86 97 0 1602 215 1387 1.494 1595 1379 .669 1.459 .58 .545
3 3026 2229 89 190 2937 2039 3322 2348 99 204 3233 2158 0 0 945 773 48 77 100 99 98 97 4976 5391 1.44 .694 .667 .687 .681 1.442 120 434 .702 .97 120 2640 8990 64 76 101 113 0 2449 209 2241 .763 2580 2371 1.311 .734 -.39 -.447
4 2185 3125 88 186 2097 2939 2292 3233 96 211 2204 3047 0 0 739 1040 44 145 100 100 100 99 5036 5251 .714 1.402 1.382 1.428 1.404 1.225 120 406 1.406 .98 120 2790 8990 64 76 116 128 0 3434 204 3230 1.54 3553 3348 .649 1.519 .623 .603
5 9676 8028 90 192 9586 7836 10515 8571 94 231 10425 8379 0 0 3104 2652 33 290 100 100 100 100 17422 18804 1.223 .817 .804 .826 .799 1.218 120 481 .817 .98 130 2960 8990 63 76 132 145 0 8822 211 8611 .898 9419 9208 1.113 .883 -.155 -.179
6 1120 2309 91 197 1029 2112 1133 2274 94 243 1042 2077 0 0 210 500 31 342 100 100 100 100 3141 3119 .487 2.052 1.993 2.04 2.076 1.243 80 351 2.259 .9 110 3120 8980 63 74 149 160 0 2537 216 2321 2.255 2499 2282 .443 2.19 1.173 1.131
7 8230 3495 92 195 8138 3300 7950 3189 101 237 7858 2994 0 0 3916 1724 47 240 99 99 98 96 11438 10852 2.466 .406 .381 .424 .394 1.543 120 427 .405 .97 120 3270 8980 63 75 164 176 0 3841 214 3626 .446 3504 3290 2.244 .419 -1.166 -1.256
8 1329 2252 91 192 1238 2060 1308 2183 101 230 1217 1991 0 0 298 488 48 196 100 100 100 100 3298 3208 .601 1.664 1.636 1.669 1.681 1.258 80 387 1.689 .96 110 3430 8980 63 74 180 191 0 2475 211 2264 1.829 2399 2188 .547 1.798 .871 .846
9 2612 4601 92 190 2520 4411 2539 4441 94 210 2447 4251 0 0 614 1215 20 127 100 100 100 100 6931 6698 .571 1.75 1.737 1.731 1.718 1.203 80 392 1.77 .98 110 3580 8980 63 74 195 206 0 5056 209 4847 1.924 4880 4671 .52 1.909 .944 .933
10 1068 1324 92 187 976 1137 1113 1327 94 201 1021 1140 0 0 345 463 20 119 100 98 100 98 2113 2161 .858 1.165 1.117 1.137 1.141 1.293 120 453 1.206 .96 120 3740 8980 63 75 211 223 0 1455 205 1249 1.28 1458 1253 .781 1.227 .356 .295
11 1321 10510 93 195 1228 10315 1361 10777 95 214 1268 10582 0 0 542 4457 20 251 99 100 99 100 11543 11850 .119 8.4 8.345 8.607 8.436 1.253 120 442 9.09 .97 120 3900 8980 63 75 227 239 0 11549 214 11335 9.231 11843 11629 .108 9.171 3.206 3.197
12 640 1674 94 195 546 1479 650 1678 95 218 556 1483 0 0 210 506 20 252 100 99 98 97 2025 2039 .369 2.709 2.667 2.778 2.702 1.334 120 440 2.758 .95 120 4060 8980 63 75 243 255 0 1840 214 1625 2.977 1844 1630 .336 2.931 1.574 1.551
13 1545 3163 93 194 1452 2969 1653 3237 95 201 1560 3043 0 0 447 953 19 75 100 100 100 100 4421 4603 .489 2.045 1.951 2.059 2.003 1.243 120 444 2.085 .98 120 4220 8980 63 75 259 271 0 3476 213 3263 2.247 3557 3344 .445 2.144 1.168 1.1
14 1064 2413 95 199 969 2214 1115 2420 97 216 1020 2221 0 0 364 900 19 145 100 100 100 100 3183 3241 .438 2.285 2.177 2.282 2.294 1.309 80 324 2.365 .96 100 4370 8980 64 74 275 285 0 2652 219 2433 2.511 2659 2441 .398 2.393 1.328 1.259
15 5468 3068 95 203 5373 2865 5884 3249 102 246 5789 3046 0 0 1745 1031 56 623 100 95 100 89 8238 8835 1.875 .533 .526 .53 .518 1.281 120 452 .531 .97 120 4530 8980 63 75 290 302 0 3371 223 3148 .586 3570 3347 1.707 .578 -.771 -.79
16 836 1144 93 188 743 956 824 1099 95 209 731 911 0 0 209 333 20 118 100 100 100 100 1699 1642 .777 1.287 1.246 1.263 1.29 1.338 80 356 1.337 .94 110 4680 8990 64 75 305 316 0 1257 207 1051 1.414 1208 1001 .707 1.369 .5 .454
17 577 638 92 185 485 453 581 601 95 244 489 416 0 0 113 180 21 458 100 42 100 0 938 905 1.071 .934 .851 .884 .927 1.506 80 394 5.777 .33 110 4850 8990 64 75 322 333 0 701 203 498 1.026 660 457 .974 .935 .038 -.097
18 958 2982 99 190 859 2792 959 2981 116 213 860 2791 0 0 142 657 84 144 100 100 100 100 3651 3651 .308 3.25 3.245 3.201 3.172 1.223 80 376 3.372 .96 110 5000 8990 64 75 337 348 0 3277 209 3068 3.572 3276 3067 .28 3.566 1.837 1.834
19 1013 740 99 193 914 547 1045 756 120 207 946 563 0 0 265 238 94 93 100 96 100 92 1461 1509 1.671 .598 .595 .571 .604 1.57 52 255 .62 .89 80 5140 8970 64 72 353 361 0 813 212 601 .658 831 619 1.521 .654 -.605 -.613
20 997 1549 98 190 899 1359 1046 1589 107 199 948 1399 0 0 326 458 62 85 97 99 95 98 2258 2347 .662 1.512 1.476 1.57 1.483 1.517 120 495 1.791 .84 120 5310 8990 64 76 368 380 0 1702 209 1493 1.661 1746 1537 .602 1.622 .732 .697

Total number of rows: 37632

Table truncated, full table size 8391 Kbytes.




Supplementary data files not provided
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