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Sample GSM84875 Query DataSets for GSM84875
Status Public on Nov 23, 2005
Title s9797, p635, 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 s9797, p635, CPT
Organism Homo sapiens
Characteristics s9797, p635, CPT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25802.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 1899 3449 339 194 1560 3255 1935 3469 350 203 1596 3275 0 0 241 562 84 60 100 100 100 100 4815 4871 .479 2.087 2.052 2.078 2.102 1.179 80 431 2.167 .94 100 2480 8780 28 38 39 49 0 2653 149 2504 1.605 2668 2519 .623 1.578 .683 .659
2 1969 3459 328 184 1641 3275 1958 3575 339 191 1630 3391 0 0 241 513 82 59 100 100 100 100 4916 5021 .501 1.996 2.08 1.989 1.984 1.192 80 435 2.025 .95 110 2630 8770 26 37 53 64 0 2661 142 2519 1.535 2750 2608 .651 1.6 .618 .678
3 1439 1936 316 179 1123 1757 1438 1937 326 184 1122 1758 0 0 210 319 76 56 100 100 100 100 2880 2880 .639 1.565 1.567 1.567 1.581 1.216 80 423 1.585 .95 110 2790 8780 27 38 69 80 0 1489 138 1352 1.204 1490 1352 .831 1.205 .267 .269
4 2373 4293 319 181 2054 4112 2428 4601 330 187 2109 4420 0 0 396 1004 86 59 100 100 100 100 6166 6529 .5 2.002 2.096 1.967 2 1.212 80 442 2.083 .96 110 2950 8770 26 37 85 96 0 3302 139 3163 1.54 3539 3400 .649 1.612 .623 .689
5 968 735 320 183 648 552 945 732 330 191 625 549 0 0 149 127 84 65 100 100 100 100 1200 1174 1.174 .852 .878 .85 .797 1.363 80 366 .805 .86 100 3110 8770 27 37 102 112 0 565 141 425 .655 563 422 1.526 .676 -.61 -.566
6 2015 5050 326 188 1689 4862 2047 5264 334 191 1721 5076 0 0 350 955 71 52 100 100 100 100 6551 6797 .347 2.879 2.949 2.873 2.861 1.182 80 389 2.944 .96 110 3260 8780 27 38 116 127 0 3885 145 3740 2.214 4049 3905 .452 2.269 1.147 1.182
7 2795 5535 331 190 2464 5345 2871 5853 336 196 2540 5663 0 0 430 1137 72 64 100 100 100 100 7809 8203 .461 2.169 2.23 2.146 2.137 1.151 80 430 2.199 .97 110 3410 8780 27 38 131 142 0 4258 146 4112 1.669 4502 4356 .599 1.715 .739 .778
8 1409 1643 317 189 1092 1454 1431 1704 328 197 1114 1515 0 0 187 275 71 64 100 100 100 100 2546 2629 .751 1.332 1.36 1.322 1.334 1.226 80 379 1.382 .95 100 3580 8770 27 37 149 159 0 1264 145 1118 1.024 1311 1165 .976 1.046 .035 .065
9 1363 1852 320 187 1043 1665 1364 1819 331 193 1044 1632 0 0 186 287 78 66 100 100 100 100 2708 2676 .626 1.596 1.563 1.597 1.617 1.245 80 395 1.605 .92 110 3720 8780 27 38 162 173 0 1425 144 1281 1.228 1399 1255 .814 1.202 .296 .266
10 3303 4737 324 187 2979 4550 3318 5039 329 196 2994 4852 0 0 881 1294 79 66 100 100 100 100 7529 7846 .655 1.527 1.621 1.532 1.502 1.316 80 425 1.535 .96 110 3880 8780 27 38 178 189 0 3644 144 3500 1.175 3876 3732 .851 1.247 .233 .318
11 2388 3282 317 182 2071 3100 2437 3383 317 191 2120 3201 0 0 360 633 66 84 100 100 100 100 5171 5321 .668 1.497 1.51 1.484 1.491 1.186 80 434 1.525 .96 110 4040 8770 26 37 194 205 0 2525 140 2385 1.151 2602 2462 .868 1.161 .203 .216
12 2534 3438 312 180 2222 3258 2604 3545 317 188 2292 3365 0 0 415 687 66 85 100 100 100 100 5480 5657 .682 1.466 1.468 1.455 1.451 1.167 80 356 1.47 .97 100 4200 8780 28 38 211 221 0 2645 138 2506 1.128 2727 2588 .887 1.129 .174 .175
13 1903 2676 307 178 1596 2498 1882 2772 317 180 1575 2594 0 0 237 472 72 51 100 100 100 100 4094 4169 .639 1.565 1.647 1.551 1.593 1.22 80 382 1.571 .95 110 4350 8780 27 38 225 236 0 2058 137 1922 1.204 2132 1995 .831 1.267 .268 .341
14 7022 11159 311 184 6711 10975 7317 11890 319 189 7006 11706 0 0 1474 2849 68 68 100 100 100 100 17686 18712 .611 1.635 1.671 1.611 1.625 1.148 80 417 1.654 .98 110 4500 8780 27 38 240 251 0 8584 142 8442 1.258 9146 9005 .795 1.285 .331 .362
15 2556 3410 309 186 2247 3224 2641 3572 315 193 2332 3386 0 0 431 710 68 70 100 100 100 100 5471 5718 .697 1.435 1.452 1.423 1.417 1.192 80 347 1.459 .96 100 4670 8780 28 38 258 268 0 2623 143 2480 1.104 2748 2605 .906 1.117 .142 .16
16 2599 7358 302 177 2297 7181 2890 8412 311 183 2588 8235 0 0 928 2819 73 51 99 100 97 100 9478 10823 .32 3.126 3.182 3.217 3.163 1.485 120 432 3.169 .97 120 4820 8780 27 39 272 284 0 5660 136 5524 2.405 6471 6335 .416 2.448 1.266 1.291
17 3640 3900 291 168 3349 3732 3798 4165 296 174 3507 3997 0 0 732 880 65 49 100 100 100 100 7081 7504 .897 1.114 1.14 1.109 1.144 1.176 80 335 1.121 .96 100 4980 8780 28 38 289 299 0 3000 129 2871 .857 3204 3075 1.167 .877 -.222 -.19
18 2419 1688 300 166 2119 1522 2439 1718 305 172 2139 1552 0 0 427 302 66 47 100 100 100 100 3641 3691 1.392 .718 .726 .72 .718 1.273 80 363 .671 .95 110 5130 8780 27 38 303 314 0 1298 128 1171 .553 1322 1194 1.81 .558 -.856 -.841
19 563 358 295 165 268 193 322 209 303 169 27 44 0 0 510 326 65 44 33 48 25 37 461 71 1.389 .72 1.63 .753 .719 4.177 80 375 .623 .89 100 5270 8770 27 37 318 328 -50 275 127 148 .554 161 34 1.805 1.254 -.852 .326
20 2479 3159 295 170 2184 2989 2601 3317 297 174 2306 3147 0 0 721 914 63 43 100 100 100 100 5173 5453 .731 1.369 1.365 1.376 1.336 1.308 80 382 1.347 .94 100 5450 8780 28 38 336 346 0 2430 131 2299 1.053 2552 2421 .95 1.05 .074 .07

Total number of rows: 37632

Table truncated, full table size 8761 Kbytes.




Supplementary data files not provided
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