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Sample GSM84881 Query DataSets for GSM84881
Status Public on Nov 23, 2005
Title s5087, p457, Pax
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 s5087, p457, Pax
Organism Homo sapiens
Characteristics s5087, p457, Pax
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25807.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 3053 4198 389 219 2664 3979 3097 4360 396 230 2708 4141 0 0 536 988 85 84 100 100 100 100 6643 6849 .67 1.494 1.529 1.466 1.547 1.207 80 496 1.511 .98 110 2310 8350 25 36 31 42 0 3385 177 3209 1.205 3516 3340 .83 1.233 .268 .302
2 3377 7577 382 217 2995 7360 3432 7909 388 234 3050 7692 0 0 483 1246 86 103 100 100 100 100 10355 10742 .407 2.457 2.522 2.452 2.484 1.122 80 431 2.464 .99 110 2470 8340 24 35 47 58 0 6110 175 5935 1.982 6378 6203 .505 2.034 .987 1.024
3 2611 4847 370 212 2241 4635 2631 4875 378 230 2261 4663 0 0 234 514 81 106 100 100 100 100 6876 6924 .483 2.068 2.062 2.066 2.09 1.13 80 421 2.093 .99 110 2630 8340 24 35 63 74 0 3909 171 3738 1.668 3931 3760 .6 1.663 .738 .734
4 4260 8492 371 213 3889 8279 4516 9265 384 233 4145 9052 0 0 887 2235 93 130 100 100 100 100 12168 13197 .47 2.129 2.184 2.074 2.137 1.177 80 397 2.154 .99 110 2780 8340 24 35 78 89 0 6848 172 6677 1.717 7472 7300 .582 1.761 .78 .817
5 1446 1005 372 225 1074 780 1443 1008 382 237 1071 783 0 0 214 204 88 114 100 100 100 100 1854 1854 1.377 .726 .731 .716 .72 1.28 80 403 .746 .93 110 2930 8340 24 35 93 104 0 810 181 629 .586 813 631 1.707 .59 -.772 -.762
6 2970 13152 364 217 2606 12935 3085 14091 372 233 2721 13874 0 0 535 2898 72 103 100 100 100 100 15541 16595 .201 4.964 5.099 4.926 4.918 1.128 80 412 4.999 .99 110 3080 8340 24 35 108 119 0 10606 175 10431 4.003 11364 11189 .25 4.112 2.001 2.04
7 4005 8616 360 201 3645 8415 4228 9646 370 222 3868 9445 0 0 758 2282 89 139 100 100 100 100 12060 13313 .433 2.309 2.442 2.256 2.31 1.166 80 422 2.362 .99 110 3230 8340 24 35 123 134 0 6948 162 6786 1.862 7779 7617 .537 1.969 .897 .978
8 2158 2769 353 203 1805 2566 2209 2907 363 215 1856 2704 0 0 299 456 87 112 100 100 100 100 4371 4560 .703 1.422 1.457 1.416 1.431 1.154 80 375 1.421 .98 100 3390 8340 25 35 140 150 0 2233 164 2069 1.146 2344 2181 .872 1.175 .197 .233
9 1684 2041 357 196 1327 1845 1695 2027 365 214 1338 1831 0 0 213 350 86 98 100 100 100 100 3172 3169 .719 1.39 1.368 1.384 1.402 1.237 80 412 1.408 .96 110 3540 8340 24 35 154 165 0 1646 158 1488 1.121 1635 1477 .892 1.104 .165 .142
10 3871 6630 355 190 3516 6440 4143 7264 368 209 3788 7074 0 0 893 1867 97 112 100 100 100 100 9956 10862 .546 1.832 1.867 1.803 1.84 1.154 80 378 1.862 .99 100 3700 8340 25 35 171 181 0 5347 153 5194 1.477 5858 5705 .677 1.506 .563 .591
11 3113 4574 349 183 2764 4391 3202 4720 353 190 2853 4537 0 0 470 787 68 67 100 100 100 100 7155 7390 .629 1.589 1.59 1.585 1.573 1.125 80 441 1.572 .99 110 3860 8340 24 35 186 197 0 3689 148 3541 1.281 3806 3659 .781 1.282 .357 .359
12 3160 5156 361 194 2799 4962 3267 5606 365 204 2906 5412 0 0 612 1357 66 69 100 100 100 100 7761 8318 .564 1.773 1.862 1.728 1.794 1.183 80 438 1.792 .99 110 4020 8350 25 36 202 213 0 4158 156 4002 1.43 4521 4365 .699 1.502 .516 .587
13 2784 4141 377 200 2407 3941 2837 4286 376 210 2460 4086 0 0 332 743 68 71 100 100 100 100 6348 6546 .611 1.637 1.661 1.62 1.629 1.149 80 416 1.626 .98 110 4190 8340 24 35 219 230 0 3340 161 3178 1.32 3456 3295 .757 1.339 .401 .422
14 11731 13054 378 220 11353 12834 12484 14185 389 234 12106 13965 0 0 2702 4049 143 137 100 100 100 100 24187 26071 .885 1.13 1.154 1.081 1.157 1.22 80 404 1.155 .99 110 4330 8340 24 35 233 244 0 10527 177 10350 .912 11440 11262 1.097 .93 -.133 -.104
15 3491 5048 373 228 3118 4820 3567 5326 386 247 3194 5098 0 0 535 1042 150 147 100 100 100 100 7938 8292 .647 1.546 1.596 1.526 1.535 1.154 80 341 1.546 .98 100 4500 8350 26 36 251 261 0 4071 184 3887 1.247 4295 4111 .802 1.287 .318 .364
16 4084 14546 359 206 3725 14340 4734 17448 361 208 4375 17242 0 0 1457 5961 61 65 99 100 98 100 18065 21617 .26 3.85 3.941 3.874 3.831 1.252 120 424 3.929 .99 120 4650 8340 24 36 265 277 0 11731 166 11565 3.105 14071 13905 .322 3.178 1.634 1.668
17 6060 3490 358 198 5702 3292 6286 3731 363 199 5928 3533 0 0 1155 848 71 54 100 100 100 100 8994 9461 1.732 .577 .596 .564 .571 1.173 80 379 .576 .98 110 4800 8340 24 35 280 291 0 2815 160 2655 .466 3009 2849 2.148 .481 -1.103 -1.057
18 3343 3013 351 188 2992 2825 3404 3079 359 200 3053 2891 0 0 451 507 78 70 100 100 100 100 5817 5944 1.059 .944 .947 .939 .944 1.164 80 415 .937 .98 110 4960 8330 23 34 296 307 0 2430 152 2278 .761 2483 2331 1.313 .764 -.393 -.389
19 787 403 345 180 442 223 387 231 353 193 42 51 0 0 710 338 81 72 41 45 36 36 665 93 1.982 .505 1.214 .53 .473 2.737 80 363 .479 .93 100 5100 8340 25 35 311 321 -50 325 145 180 .407 186 41 2.458 .979 -1.297 -.03
20 4646 3148 368 196 4278 2952 4629 3178 409 231 4261 2982 0 0 901 643 251 170 100 100 100 100 7230 7243 1.449 .69 .7 .688 .676 1.135 52 346 .685 .98 90 5270 8330 24 33 328 337 0 2539 158 2381 .556 2563 2405 1.797 .564 -.846 -.825

Total number of rows: 37632

Table truncated, full table size 8799 Kbytes.




Supplementary data files not provided
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