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Sample GSM84949 Query DataSets for GSM84949
Status Public on Nov 23, 2005
Title s7609, p451, 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 s7609, p451, Pax whole blood
Organism Homo sapiens
Characteristics s7609, p451, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23019.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 1416 2039 176 110 1240 1929 1472 2085 180 112 1296 1975 0 0 350 487 34 25 100 100 100 100 3169 3271 .643 1.556 1.524 1.57 1.577 1.192 80 373 1.541 .98 100 2310 8150 27 37 28 38 0 1618 87 1531 1.235 1655 1567 .81 1.209 .304 .274
2 1418 3408 178 119 1240 3289 1470 3413 182 126 1292 3294 0 0 418 1094 36 48 100 100 100 100 4529 4586 .377 2.652 2.55 2.673 2.678 1.192 80 465 2.64 .98 110 2470 8140 25 36 43 54 0 2705 94 2610 2.105 2709 2614 .475 2.023 1.074 1.017
3 1093 3090 184 130 909 2960 1091 3062 190 141 907 2932 0 0 218 628 40 53 100 100 100 100 3869 3839 .307 3.256 3.233 3.279 3.252 1.185 80 465 3.269 .98 110 2630 8140 25 36 59 70 0 2452 103 2349 2.584 2430 2327 .387 2.566 1.37 1.359
4 1623 2953 185 130 1438 2823 1595 2981 189 142 1410 2851 0 0 409 702 39 46 100 100 100 100 4261 4261 .509 1.963 2.022 1.981 1.944 1.199 80 390 1.947 .97 100 2790 8150 27 37 76 86 0 2344 103 2240 1.558 2366 2263 .642 1.605 .64 .682
5 808 797 182 127 626 670 792 714 187 132 610 587 0 0 227 285 39 40 100 100 100 100 1296 1197 .934 1.07 .962 1.062 1.022 1.323 80 420 1.086 .94 110 2950 8140 25 36 91 102 0 633 101 532 .849 567 466 1.177 .764 -.235 -.389
6 1170 4345 185 125 985 4220 1213 4402 191 132 1028 4277 0 0 424 1700 48 41 98 100 96 100 5205 5305 .233 4.284 4.161 4.439 4.351 1.377 120 458 4.35 .97 120 3110 8140 25 37 107 119 0 3448 99 3349 3.4 3494 3394 .294 3.302 1.766 1.723
7 2599 4382 188 139 2411 4243 2646 4441 197 149 2458 4302 0 0 748 1051 52 50 100 100 100 100 6654 6760 .568 1.76 1.75 1.805 1.776 1.196 80 385 1.716 .98 110 3270 8140 25 36 123 134 0 3478 110 3367 1.397 3525 3414 .716 1.389 .482 .474
8 1499 2304 187 136 1312 2168 1504 2331 193 143 1317 2195 0 0 258 421 40 45 100 100 100 100 3480 3512 .605 1.652 1.667 1.65 1.65 1.184 80 347 1.625 .97 100 3420 8140 26 36 139 149 0 1829 108 1721 1.311 1850 1742 .763 1.323 .391 .404
9 2690 3697 186 128 2504 3569 2521 3476 193 139 2335 3348 0 0 999 1168 65 84 100 100 100 100 6073 5683 .702 1.425 1.434 1.449 1.473 1.229 80 423 1.386 .96 110 3570 8140 25 36 153 164 0 2934 102 2833 1.131 2759 2657 .884 1.138 .178 .186
10 2960 3734 185 129 2775 3605 2861 3887 195 139 2676 3758 0 0 1067 1190 67 85 100 100 100 100 6380 6434 .77 1.299 1.404 1.329 1.331 1.205 80 425 1.279 .98 110 3740 8140 25 36 170 181 0 2963 102 2861 1.031 3085 2983 .97 1.115 .044 .156
11 3415 4427 185 129 3230 4298 3488 4355 195 145 3303 4226 0 0 1234 1246 63 76 100 100 100 100 7528 7529 .752 1.331 1.279 1.383 1.357 1.231 80 420 1.279 .98 110 3900 8130 24 35 186 197 0 3513 102 3411 1.056 3456 3354 .947 1.015 .079 .022
12 2911 3769 200 134 2711 3635 2927 3557 206 153 2727 3423 0 0 1202 1523 65 76 100 100 100 100 6346 6150 .746 1.341 1.255 1.375 1.326 1.215 80 335 1.321 .98 100 4050 8140 26 36 202 212 0 2991 106 2885 1.064 2823 2717 .94 .996 .09 -.005
13 2092 2883 195 128 1897 2755 1911 2542 199 139 1716 2414 0 0 832 1028 49 50 100 100 100 100 4652 4130 .689 1.452 1.407 1.49 1.448 1.242 80 410 1.394 .97 110 4200 8140 25 36 216 227 0 2288 102 2187 1.153 2017 1916 .868 1.116 .205 .159
14 4801 4304 198 133 4603 4171 4822 4313 217 146 4624 4180 0 0 1539 1209 90 64 100 100 100 100 8774 8804 1.104 .906 .904 .919 .896 1.185 80 421 .89 .98 110 4360 8130 24 35 232 243 0 3416 106 3310 .719 3423 3317 1.391 .717 -.476 -.479
15 2726 3534 199 138 2527 3396 2668 3508 221 153 2469 3370 0 0 785 916 89 67 100 100 100 100 5923 5839 .744 1.344 1.365 1.362 1.348 1.202 80 411 1.333 .97 110 4510 8140 25 36 247 258 0 2805 110 2695 1.067 2784 2675 .938 1.083 .093 .115
16 2006 9831 192 135 1814 9696 1943 10121 203 206 1751 9986 0 0 597 2226 60 195 100 100 100 100 11510 11737 .187 5.345 5.703 5.475 5.423 1.267 80 435 5.178 .97 110 4670 8130 24 35 263 274 0 7802 107 7695 4.242 8033 7925 .236 4.526 2.085 2.178
17 2673 1710 183 123 2490 1587 2677 1619 196 196 2494 1496 0 0 932 650 62 199 100 100 100 100 4077 3990 1.569 .637 .6 .632 .607 1.25 80 411 .632 .96 110 4830 8140 25 36 279 290 0 1357 98 1260 .506 1285 1187 1.977 .476 -.983 -1.071
18 1426 2019 172 110 1254 1909 1383 1960 181 119 1211 1850 0 0 455 577 47 40 100 100 100 100 3163 3061 .657 1.522 1.528 1.567 1.527 1.283 80 440 1.495 .97 110 4990 8140 25 36 295 306 0 1602 87 1515 1.208 1556 1468 .828 1.212 .273 .278
19 869 500 177 107 692 393 832 433 174 109 655 326 0 0 420 175 35 29 100 100 100 100 1085 981 1.761 .568 .498 .646 .61 1.577 12 104 .528 .91 50 5130 8140 28 33 312 317 0 397 85 312 .451 344 259 2.219 .395 -1.15 -1.34
20 2425 1887 178 116 2247 1771 2506 1938 186 117 2328 1822 0 0 907 684 50 28 100 100 100 100 4018 4150 1.269 .788 .783 .799 .788 1.233 52 344 .776 .97 90 5290 8130 25 34 326 335 0 1498 92 1406 .626 1538 1446 1.599 .621 -.677 -.687

Total number of rows: 37632

Table truncated, full table size 8692 Kbytes.




Supplementary data files not provided
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