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Sample GSM84919 Query DataSets for GSM84919
Status Public on Nov 23, 2005
Title s8376, p963, 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 s8376, p963, Pax whole blood
Organism Homo sapiens
Characteristics s8376, p963, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23003.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 2373 4682 297 294 2076 4388 2292 4825 314 324 1995 4531 0 0 1015 1945 110 161 100 100 100 100 6464 6526 .473 2.114 2.271 2.197 2.185 1.264 52 279 2.077 .98 80 2160 8450 32 40 50 58 0 3101 195 2906 1.4 3195 3001 .714 1.504 .485 .589
2 2193 5102 272 294 1921 4808 2249 5547 285 311 1977 5253 0 0 891 1957 102 136 100 100 100 100 6729 7230 .4 2.503 2.657 2.564 2.52 1.209 80 470 2.481 .98 110 2320 8450 30 41 64 75 0 3379 195 3184 1.658 3674 3479 .603 1.76 .729 .815
3 2497 7496 256 318 2241 7178 2601 8109 269 345 2345 7791 0 0 1042 2665 81 149 100 100 100 100 9419 10136 .312 3.203 3.322 3.395 3.322 1.246 52 267 3.129 .98 80 2470 8450 32 40 81 89 0 4964 211 4754 2.121 5370 5160 .471 2.2 1.085 1.138
4 2238 5039 275 324 1963 4715 2663 5729 284 354 2388 5405 0 0 1224 2662 91 162 91 97 87 91 6678 7793 .416 2.402 2.263 2.592 2.416 1.29 80 401 2.312 .98 100 2630 8460 32 42 96 106 0 3337 215 3123 1.591 3794 3579 .629 1.499 .67 .584
5 2357 4992 274 328 2083 4664 2163 4586 293 371 1889 4258 0 0 1051 1979 122 189 100 100 100 100 6747 6147 .447 2.239 2.254 2.34 2.332 1.25 52 323 2.182 .98 90 2780 8460 32 41 111 120 0 3306 217 3089 1.483 3037 2820 .674 1.493 .568 .578
6 1903 7297 205 263 1698 7034 1949 8028 226 291 1744 7765 0 0 716 2346 79 131 100 100 100 100 8732 9509 .241 4.143 4.452 4.334 4.218 1.266 80 445 4.047 .98 110 2950 8440 29 40 127 138 0 4832 174 4658 2.743 5317 5142 .365 2.949 1.456 1.56
7 3020 7347 183 227 2837 7120 3074 7292 186 234 2891 7065 0 0 965 2195 37 66 100 100 100 100 9957 9956 .398 2.51 2.444 2.539 2.547 1.166 80 408 2.478 .98 110 3110 8440 29 40 143 154 0 4866 150 4715 1.662 4829 4679 .602 1.618 .733 .695
8 2290 5806 186 222 2104 5584 2071 5719 187 228 1885 5497 0 0 769 1669 35 60 100 100 100 100 7688 7382 .377 2.654 2.916 2.705 2.72 1.225 80 417 2.611 .97 110 3260 8440 29 40 158 169 0 3845 147 3698 1.758 3787 3640 .569 1.931 .814 .95
9 2282 3892 182 223 2100 3669 2337 3869 199 258 2155 3646 0 0 489 836 128 220 100 100 100 100 5769 5801 .572 1.747 1.692 1.76 1.742 1.28 80 415 1.771 .96 110 3420 8430 28 39 174 185 0 2577 148 2430 1.157 2562 2415 .864 1.12 .21 .164
10 1833 4070 184 231 1649 3839 1862 4059 203 263 1678 3828 0 0 663 1477 130 216 100 100 100 100 5488 5506 .43 2.328 2.281 2.342 2.315 1.196 80 398 2.333 .98 110 3570 8440 29 40 189 200 0 2695 153 2542 1.542 2688 2535 .649 1.511 .625 .595
11 1929 3810 183 218 1746 3592 1970 3793 201 252 1787 3575 0 0 533 1015 115 216 100 100 100 100 5338 5362 .486 2.057 2.001 2.087 2.032 1.251 80 416 2.06 .97 110 3730 8430 28 39 205 216 0 2523 144 2379 1.362 2512 2368 .734 1.325 .446 .406
12 1537 3385 179 212 1358 3173 1503 3183 195 247 1324 2971 0 0 656 1518 105 207 100 100 100 100 4531 4295 .428 2.337 2.244 2.365 2.369 1.331 80 423 2.377 .96 110 3880 8440 29 40 220 231 0 2242 140 2101 1.547 2108 1968 .646 1.486 .63 .571
13 1536 3139 184 213 1352 2926 1542 2999 188 226 1358 2786 0 0 501 991 39 75 100 100 100 100 4278 4144 .462 2.164 2.052 2.203 2.134 1.365 80 443 2.186 .96 110 4050 8430 28 39 237 248 0 2079 141 1938 1.433 1986 1845 .698 1.359 .519 .442
14 4111 4338 188 205 3923 4133 4104 4387 193 222 3916 4182 0 0 1383 1308 52 81 100 100 100 100 8056 8098 .949 1.054 1.068 1.072 1.059 1.209 80 418 1.035 .98 110 4200 8430 28 39 252 263 0 2873 136 2737 .698 2905 2770 1.433 .707 -.519 -.5
15 1808 3347 182 208 1626 3139 1864 3376 187 218 1682 3168 0 0 570 961 50 69 100 100 100 100 4765 4850 .518 1.931 1.883 1.978 1.933 1.261 80 378 1.927 .97 100 4360 8430 29 39 269 279 0 2217 138 2079 1.278 2236 2098 .782 1.247 .354 .319
16 2253 9183 178 214 2075 8969 2255 9182 183 225 2077 8968 0 0 588 2256 39 84 100 100 100 100 11044 11045 .231 4.322 4.318 4.359 4.382 1.144 80 427 4.316 .98 110 4510 8430 28 39 283 294 0 6081 142 5940 2.863 6081 5939 .349 2.859 1.517 1.516
17 2714 2137 182 208 2532 1929 2687 1980 183 220 2505 1772 0 0 878 865 43 85 100 100 100 100 4461 4277 1.313 .762 .707 .755 .706 1.435 80 435 .804 .93 110 4670 8430 28 39 299 310 0 1415 138 1277 .505 1311 1174 1.982 .468 -.987 -1.094
18 1875 4126 180 212 1695 3914 1803 3860 182 218 1623 3648 0 0 518 1289 40 56 100 100 100 100 5609 5271 .433 2.309 2.248 2.306 2.308 1.246 80 392 2.375 .96 100 4830 8430 29 39 316 326 0 2732 140 2592 1.529 2556 2416 .654 1.489 .613 .574
19 560 585 172 229 388 356 233 247 176 234 61 18 0 0 682 697 32 67 65 38 47 31 744 79 1.09 .918 .295 .963 .98 2.36 80 384 1.009 .97 100 5000 8430 29 39 333 343 -50 387 152 236 .608 164 12 1.646 .195 -.719 -2.355
20 1797 2382 176 226 1621 2156 1755 1748 180 232 1579 1522 0 0 847 1857 35 63 100 100 100 100 3777 3101 .752 1.33 .964 1.171 1.092 1.585 52 310 1.676 .88 90 5140 8430 29 38 347 356 0 1577 150 1428 .881 1158 1008 1.135 .638 -.183 -.648

Total number of rows: 37632

Table truncated, full table size 8739 Kbytes.




Supplementary data files not provided
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