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Sample GSM84844 Query DataSets for GSM84844
Status Public on Nov 23, 2005
Title s8356, p377, 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 s8356, p377, Pax whole blood
Organism Homo sapiens
Characteristics s8356, p377, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23033.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
1 803 1070 141 117 662 953 837 1162 148 131 696 1045 0 0 423 476 40 71 88 97 86 93 1615 1741 .695 1.44 1.501 1.642 1.414 2.138 80 388 1.339 .91 100 2020 8170 24 34 37 47 0 843 92 750 1.134 915 823 .882 1.182 .181 .242
2 1074 1647 140 116 934 1531 1155 1728 143 122 1015 1612 0 0 503 698 28 45 100 100 97 98 2465 2627 .61 1.639 1.588 1.758 1.713 1.441 120 502 1.59 .97 120 2180 8170 23 35 52 64 0 1297 91 1206 1.291 1361 1269 .775 1.251 .368 .323
3 806 1889 141 121 665 1768 811 1959 145 127 670 1838 0 0 318 634 30 63 98 100 97 100 2433 2508 .376 2.659 2.743 2.894 2.662 1.475 80 430 2.459 .95 110 2330 8180 24 35 67 78 0 1487 95 1392 2.093 1543 1447 .478 2.16 1.066 1.111
4 910 1273 144 124 766 1149 1098 1448 149 134 954 1324 0 0 471 565 63 69 87 98 83 92 1915 2278 .667 1.5 1.388 1.65 1.483 1.897 80 430 1.397 .94 110 2500 8170 23 34 84 95 0 1002 98 905 1.181 1140 1043 .847 1.093 .24 .128
5 552 587 142 124 410 463 514 558 145 132 372 434 0 0 203 248 34 53 100 97 97 96 873 806 .886 1.129 1.167 1.104 1.09 1.506 80 386 1.171 .92 110 2640 8170 23 34 98 109 0 462 98 365 .889 439 342 1.125 .919 -.169 -.122
6 936 1943 143 129 793 1814 973 2051 150 142 830 1922 0 0 573 1005 61 72 82 96 81 95 2607 2752 .437 2.288 2.316 2.161 2.172 1.853 80 387 2.111 .92 110 2800 8170 23 34 114 125 0 1530 102 1428 1.801 1615 1513 .555 1.823 .849 .867
7 1667 2519 144 124 1523 2395 1792 2580 149 137 1648 2456 0 0 746 896 58 73 92 100 92 100 3918 4104 .636 1.573 1.49 1.658 1.555 1.471 80 405 1.518 .95 110 2960 8160 22 33 130 141 0 1983 98 1886 1.238 2031 1934 .808 1.173 .308 .231
8 973 1340 144 124 829 1216 969 1320 152 134 825 1196 0 0 198 243 111 96 100 100 100 100 2045 2021 .682 1.467 1.45 1.483 1.429 1.248 80 367 1.407 .96 100 3110 8170 24 34 146 156 0 1055 98 957 1.155 1039 942 .866 1.141 .208 .191
9 1623 1783 137 124 1486 1659 1814 2003 145 132 1677 1879 0 0 1049 978 96 85 84 94 80 92 3145 3556 .896 1.116 1.12 1.343 1.099 1.916 120 509 1.042 .96 120 3280 8160 22 34 162 174 0 1404 98 1306 .879 1577 1480 1.138 .882 -.186 -.181
10 1880 2700 127 119 1753 2581 2118 2806 190 162 1991 2687 0 0 1007 1238 522 368 82 98 72 91 4334 4678 .679 1.472 1.35 1.694 1.479 1.658 80 367 1.408 .97 100 3450 8170 24 34 180 190 0 2126 94 2032 1.159 2209 2116 .863 1.063 .213 .088
11 1679 2208 127 121 1552 2087 1786 2304 186 163 1659 2183 0 0 930 792 503 356 88 95 75 91 3639 3842 .744 1.345 1.316 1.529 1.371 1.632 80 395 1.192 .94 110 3600 8160 22 33 194 205 0 1739 95 1643 1.059 1814 1719 .944 1.036 .082 .051
12 1593 2249 138 125 1455 2124 1289 1882 141 133 1151 1757 0 0 1180 1465 38 49 92 98 91 98 3579 2908 .685 1.46 1.526 1.65 1.431 1.985 80 338 1.382 .96 100 3750 8160 23 33 210 220 0 1771 98 1672 1.149 1482 1383 .87 1.202 .201 .265
13 1301 1759 140 125 1161 1634 1342 1732 149 139 1202 1607 0 0 482 550 73 73 96 100 96 100 2795 2809 .711 1.407 1.337 1.502 1.344 1.671 80 412 1.383 .96 110 3890 8170 23 34 223 234 0 1385 98 1287 1.108 1364 1265 .902 1.053 .148 .074
14 4168 5137 142 128 4026 5009 4441 5302 156 144 4299 5174 0 0 1335 1422 102 79 100 100 100 100 9035 9473 .804 1.244 1.204 1.27 1.237 1.239 80 404 1.205 .97 110 4060 8170 23 34 240 251 0 4045 101 3944 .98 4175 4074 1.021 .948 -.03 -.078
15 2491 3746 140 131 2351 3615 2591 3859 149 141 2451 3728 0 0 818 1105 90 59 100 100 100 100 5966 6179 .65 1.538 1.521 1.575 1.528 1.277 80 365 1.514 .98 100 4200 8160 23 33 255 265 0 2950 103 2846 1.211 3039 2935 .826 1.198 .276 .26
16 1731 6041 134 129 1597 5912 1726 6110 138 145 1592 5981 0 0 763 2187 31 84 96 100 96 100 7509 7573 .27 3.702 3.757 3.892 3.726 1.346 80 413 3.613 .97 110 4360 8160 22 33 270 281 0 4757 102 4655 2.915 4811 4709 .343 2.958 1.543 1.565
17 1916 1312 133 128 1783 1184 1957 1375 139 142 1824 1247 0 0 851 543 74 97 100 100 98 100 2967 3071 1.506 .664 .684 .694 .681 1.444 80 413 .639 .96 110 4510 8160 22 33 285 296 0 1033 101 932 .523 1083 982 1.913 .538 -.935 -.893
18 1347 2108 135 121 1212 1987 1404 2199 136 130 1269 2078 0 0 427 563 29 46 100 100 100 100 3199 3347 .61 1.639 1.638 1.696 1.603 1.363 80 378 1.618 .96 100 4670 8160 23 33 302 312 0 1660 95 1565 1.291 1731 1636 .775 1.289 .368 .367
19 337 257 130 123 207 134 158 158 132 127 28 35 0 0 413 249 29 44 50 46 41 36 341 63 1.545 .647 1.25 .96 .97 4.261 80 381 .595 .9 100 4830 8160 23 33 318 328 -50 202 97 106 .51 124 28 1.962 .984 -.972 -.023
20 1389 1104 135 128 1254 976 1387 1014 139 135 1252 886 0 0 571 407 31 46 98 100 98 100 2230 2138 1.285 .778 .708 .859 .769 1.779 52 255 .744 .94 80 4980 8160 24 32 334 342 0 869 101 769 .613 798 698 1.632 .557 -.706 -.844

Total number of rows: 37632

Table truncated, full table size 8641 Kbytes.




Supplementary data files not provided
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