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Sample GSM84905 Query DataSets for GSM84905
Status Public on Nov 23, 2005
Title s5794, p560, CPT
Sample type RNA
 
Channel 1
Source name Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Organism Homo sapiens
Characteristics Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name s5794, p560, CPT
Organism Homo sapiens
Characteristics s5794, p560, CPT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25819.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 GPL3122
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 1693 2976 299 167 1394 2809 1857 3192 303 171 1558 3025 0 0 523 1090 56 48 100 100 100 100 4203 4583 .496 2.015 1.942 2.005 2.035 1.288 120 571 2.061 .97 120 2630 8080 28 40 37 49 0 2188 123 2065 1.482 2347 2224 .675 1.428 .567 .514
2 2335 4466 293 167 2042 4299 2339 4628 297 176 2046 4461 0 0 269 691 58 83 100 100 100 100 6341 6507 .475 2.105 2.18 2.091 2.111 1.16 80 404 2.171 .98 110 2780 8070 27 38 52 63 0 3284 123 3161 1.548 3403 3280 .646 1.603 .63 .681
3 1723 2490 291 166 1432 2324 1719 2514 295 190 1428 2348 0 0 228 461 58 128 100 100 100 100 3756 3776 .616 1.623 1.644 1.603 1.646 1.239 80 435 1.681 .96 110 2940 8060 26 37 68 79 0 1831 122 1709 1.193 1849 1726 .838 1.209 .255 .274
4 2797 5028 293 170 2504 4858 2971 5460 298 192 2678 5290 0 0 590 1334 59 139 100 100 100 100 7362 7968 .515 1.94 1.975 1.898 1.929 1.231 80 434 2.004 .97 110 3090 8070 27 38 83 94 0 3697 125 3572 1.427 4015 3890 .701 1.452 .513 .539
5 1056 917 292 171 764 746 1027 874 294 184 735 703 0 0 203 236 54 103 100 100 100 100 1510 1438 1.024 .976 .956 .965 .966 1.331 80 449 .99 .93 110 3250 8060 26 37 99 110 0 674 126 549 .718 643 517 1.393 .703 -.478 -.508
6 2061 4331 301 174 1760 4157 2131 4538 301 187 1830 4364 0 0 272 818 58 70 100 100 100 100 5917 6194 .423 2.362 2.385 2.341 2.35 1.158 80 413 2.431 .98 110 3410 8070 27 38 115 126 0 3185 128 3057 1.737 3337 3209 .576 1.753 .796 .81
7 3248 7010 301 180 2947 6830 3306 7478 303 200 3005 7298 0 0 579 1645 61 134 100 100 100 100 9777 10303 .431 2.318 2.429 2.283 2.315 1.211 80 400 2.375 .98 110 3560 8070 27 38 130 141 0 5154 132 5022 1.704 5499 5366 .587 1.786 .769 .837
8 1480 1825 299 173 1181 1652 1479 1866 306 196 1180 1693 0 0 245 430 73 141 100 100 100 100 2833 2873 .715 1.399 1.435 1.376 1.382 1.223 80 454 1.443 .96 110 3720 8060 26 37 146 157 0 1342 127 1215 1.029 1372 1245 .972 1.055 .041 .077
9 1349 2192 295 179 1054 2013 1369 2221 298 193 1074 2042 0 0 223 337 63 86 100 100 100 100 3067 3116 .524 1.91 1.901 1.932 1.872 1.23 80 413 1.878 .95 110 3880 8070 27 38 162 173 0 1612 132 1480 1.404 1633 1501 .712 1.398 .49 .483
10 4179 6253 310 199 3869 6054 4338 6825 315 211 4028 6626 0 0 1058 1623 68 78 100 100 100 100 9923 10654 .639 1.565 1.645 1.568 1.569 1.139 80 416 1.573 .98 110 4030 8070 27 38 177 188 0 4598 146 4451 1.151 5018 4872 .869 1.21 .202 .274
11 2533 3982 320 210 2213 3772 2632 4193 324 226 2312 3983 0 0 478 927 62 126 100 100 100 100 5985 6295 .587 1.704 1.723 1.684 1.702 1.191 80 423 1.748 .97 110 4180 8070 27 38 192 203 0 2928 154 2774 1.253 3083 2929 .798 1.267 .326 .341
12 2646 3816 307 193 2339 3623 2747 3935 311 212 2440 3742 0 0 641 1050 59 126 100 100 100 100 5962 6182 .646 1.549 1.534 1.536 1.552 1.168 80 446 1.582 .98 110 4340 8070 27 38 208 219 0 2806 142 2664 1.139 2893 2751 .878 1.128 .188 .173
13 2025 2789 311 190 1714 2599 2041 2810 316 210 1730 2620 0 0 297 446 65 94 100 100 100 100 4313 4350 .659 1.516 1.514 1.518 1.489 1.205 80 380 1.491 .96 110 4510 8080 28 39 225 236 0 2051 140 1911 1.115 2066 1926 .897 1.114 .157 .155
14 8205 13039 303 190 7902 12849 8998 14690 317 227 8695 14500 0 0 3447 5657 81 179 100 100 100 100 20751 23195 .615 1.626 1.668 1.617 1.647 1.316 120 429 1.644 .98 120 4660 8080 28 40 240 252 0 9588 140 9448 1.196 10801 10662 .836 1.226 .258 .294
15 3722 5102 305 194 3417 4908 3761 5340 321 262 3456 5146 0 0 805 1231 102 270 100 100 100 100 8325 8602 .696 1.436 1.489 1.426 1.398 1.243 80 390 1.476 .97 110 4820 8060 26 37 256 267 0 3751 143 3609 1.056 3926 3784 .947 1.095 .079 .131
16 2682 9298 305 196 2377 9102 2814 10235 326 271 2509 10039 0 0 987 3958 115 285 100 100 100 100 11479 12548 .261 3.829 4.001 3.781 3.812 1.287 120 524 3.933 .98 130 4980 8070 26 39 271 284 0 6837 144 6693 2.816 7526 7382 .355 2.942 1.493 1.557
17 4244 5217 304 185 3940 5032 4360 5290 321 230 4056 5105 0 0 865 1273 101 224 100 100 100 100 8972 9161 .783 1.277 1.259 1.261 1.285 1.18 80 408 1.3 .98 110 5130 8060 26 37 287 298 0 3836 136 3700 .939 3890 3754 1.065 .925 -.091 -.112
18 2904 2429 288 172 2616 2257 2818 2294 298 199 2530 2122 0 0 458 537 97 165 100 100 100 100 4873 4652 1.159 .863 .839 .852 .846 1.209 80 470 .862 .97 110 5290 8060 26 37 303 314 0 1786 126 1660 .634 1687 1560 1.576 .617 -.657 -.697
19 1167 553 243 157 924 396 1133 542 250 161 890 385 0 0 289 141 49 55 100 100 100 100 1320 1275 2.333 .429 .433 .419 .441 1.39 12 98 .475 .84 50 5440 8060 29 34 321 326 0 407 115 291 .315 399 283 3.173 .318 -1.666 -1.653
20 2764 3624 294 174 2470 3450 2933 3916 295 179 2639 3742 0 0 749 1041 59 55 100 100 100 100 5920 6381 .716 1.397 1.418 1.385 1.362 1.189 80 466 1.41 .98 110 5620 8070 27 38 336 347 0 2665 128 2537 1.027 2879 2751 .974 1.043 .038 .06

Total number of rows: 37632

Table truncated, full table size 8700 Kbytes.




Supplementary data files not provided
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