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Sample GSM84917 Query DataSets for GSM84917
Status Public on Nov 23, 2005
Title s5369, p602, Pax whole blood
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 s5369, p602, Pax whole blood
Organism Homo sapiens
Characteristics s5369, p602, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23002.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 GPL3121
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 1508 3056 168 170 1340 2886 1377 2766 171 183 1209 2596 0 0 724 1426 33 109 100 100 100 100 4226 3805 .464 2.154 2.147 2.198 2.207 1.307 80 382 2.128 .97 100 2130 8470 33 43 46 56 0 2333 130 2203 1.644 2111 1982 .608 1.639 .717 .713
2 1694 3804 166 169 1528 3635 1739 3977 170 182 1573 3808 0 0 528 1222 33 90 100 100 100 100 5163 5381 .42 2.379 2.421 2.382 2.474 1.197 80 393 2.334 .98 100 2280 8460 32 42 61 71 0 2904 129 2775 1.816 3036 2907 .551 1.848 .861 .886
3 1346 3650 169 165 1177 3485 1370 3814 172 174 1201 3649 0 0 526 1312 33 59 98 100 98 100 4662 4850 .338 2.961 3.038 3.039 2.975 1.235 80 406 2.881 .97 100 2440 8460 32 42 77 87 0 2786 126 2660 2.26 2911 2785 .442 2.319 1.176 1.214
4 1556 3171 166 165 1390 3006 1459 3064 170 177 1293 2899 0 0 710 1402 33 99 100 100 100 100 4396 4192 .462 2.163 2.242 2.249 2.11 1.276 80 458 2.143 .98 110 2600 8460 31 42 92 103 0 2421 126 2295 1.651 2339 2213 .606 1.712 .723 .775
5 858 1316 165 171 693 1145 853 1203 173 179 688 1032 0 0 185 457 40 71 100 100 100 100 1838 1720 .605 1.652 1.5 1.601 1.576 1.359 52 310 1.823 .92 90 2740 8460 32 41 107 116 0 1005 131 874 1.261 918 788 .793 1.145 .335 .195
6 1230 4187 165 166 1065 4021 1211 4321 170 180 1046 4155 0 0 324 968 39 76 100 100 100 100 5086 5201 .265 3.776 3.972 3.866 3.777 1.246 80 396 3.643 .96 100 2910 8460 32 42 124 134 0 3196 127 3069 2.882 3298 3172 .347 3.032 1.527 1.6
7 2213 3810 166 171 2047 3639 2323 3920 170 181 2157 3749 0 0 682 1088 37 67 100 100 100 100 5686 5906 .563 1.778 1.738 1.811 1.785 1.207 80 439 1.762 .98 110 3070 8450 30 41 139 150 0 2908 131 2778 1.357 2992 2862 .737 1.327 .44 .408
8 1273 2324 163 166 1110 2158 1249 2134 167 175 1086 1968 0 0 393 802 32 59 100 100 100 100 3268 3054 .514 1.944 1.812 1.936 1.888 1.293 80 369 1.861 .95 100 3230 8460 32 42 156 166 0 1774 127 1647 1.484 1629 1502 .674 1.383 .57 .468
9 1948 2308 160 169 1788 2139 1955 2219 166 182 1795 2050 0 0 613 766 48 78 100 100 100 100 3927 3845 .836 1.196 1.142 1.21 1.162 1.336 80 409 1.196 .96 110 3380 8450 30 41 170 181 0 1762 129 1633 .913 1694 1565 1.095 .872 -.131 -.198
10 1971 3034 160 166 1811 2868 2131 2894 170 190 1971 2728 0 0 833 1169 85 204 100 100 100 100 4679 4699 .631 1.584 1.384 1.643 1.6 1.278 80 369 1.567 .98 100 3540 8460 32 42 187 197 0 2316 127 2189 1.209 2209 2082 .827 1.057 .274 .079
11 2057 2871 162 172 1895 2699 2064 2790 169 190 1902 2618 0 0 651 786 74 192 98 100 98 100 4594 4520 .702 1.424 1.376 1.501 1.41 1.483 80 405 1.424 .96 110 3700 8450 30 41 202 213 0 2192 131 2060 1.087 2130 1998 .92 1.051 .121 .071
12 1607 2772 174 187 1433 2585 1612 2876 178 193 1438 2689 0 0 823 1269 38 63 100 100 100 100 4018 4127 .554 1.804 1.87 1.918 1.862 1.328 80 343 1.747 .97 100 3840 8460 32 42 217 227 0 2116 143 1973 1.377 2195 2053 .726 1.427 .462 .513
13 1551 2409 173 191 1378 2218 1478 2195 177 201 1305 2004 0 0 489 805 36 69 100 100 100 100 3596 3309 .621 1.61 1.536 1.621 1.567 1.281 80 380 1.645 .96 100 4000 8450 31 41 233 243 0 1839 146 1693 1.229 1676 1530 .814 1.172 .297 .229
14 4793 5347 166 176 4627 5171 5372 5666 171 191 5206 5490 0 0 1790 1755 34 76 100 100 100 100 9798 10696 .895 1.118 1.055 1.146 1.1 1.292 80 423 1.098 .98 110 4150 8460 31 42 247 258 0 4082 134 3947 .853 4325 4191 1.172 .805 -.229 -.313
15 1924 2924 163 174 1761 2750 2117 2975 166 180 1954 2801 0 0 721 974 32 63 100 100 100 100 4511 4755 .64 1.562 1.433 1.625 1.552 1.309 80 371 1.545 .97 100 4310 8460 32 42 264 274 0 2232 133 2099 1.192 2271 2138 .839 1.094 .253 .13
16 2494 14450 162 173 2332 14277 2569 15572 167 181 2407 15399 0 0 796 3680 36 66 98 100 97 100 16609 17806 .163 6.122 6.398 6.438 6.099 1.381 80 414 5.972 .97 110 4460 8450 30 41 278 289 0 11031 132 10898 4.673 11887 11755 .214 4.884 2.224 2.288
17 2809 1993 163 173 2646 1820 2676 1763 167 181 2513 1590 0 0 1116 877 34 62 100 100 100 100 4466 4103 1.454 .688 .633 .678 .649 1.279 80 404 .694 .95 110 4610 8460 31 42 293 304 0 1521 132 1389 .525 1346 1214 1.905 .483 -.929 -1.05
18 2181 3149 162 166 2019 2983 2410 3199 163 173 2248 3033 0 0 587 745 32 56 100 100 100 100 5002 5281 .677 1.477 1.349 1.5 1.485 1.187 80 401 1.453 .98 100 4770 8450 31 41 310 320 0 2404 127 2277 1.128 2442 2315 .887 1.03 .174 .043
19 1629 1366 160 178 1469 1188 1656 1437 163 177 1496 1259 0 0 665 645 36 54 100 100 100 91 2657 2755 1.237 .809 .842 .739 .76 1.327 12 104 .913 .94 50 4910 8450 33 38 326 331 0 1043 136 907 .617 1097 961 1.62 .642 -.696 -.638
20 2007 1770 162 168 1845 1602 1826 1500 164 179 1664 1332 0 0 976 909 37 60 100 100 100 100 3447 2996 1.152 .868 .8 .857 .851 1.407 52 344 .882 .96 90 5080 8450 31 40 341 350 0 1351 128 1223 .663 1145 1017 1.509 .611 -.593 -.711

Total number of rows: 37632

Table truncated, full table size 8739 Kbytes.




Supplementary data files not provided
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