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Sample GSM84910 Query DataSets for GSM84910
Status Public on Nov 23, 2005
Title s9146, p717, CPT
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 s9146, p717, CPT
Organism Homo sapiens
Characteristics s9146, p717, CPT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25820.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 3245 6220 327 175 2918 6045 3177 6412 348 196 2850 6237 0 0 641 1295 125 121 100 100 100 100 8963 9087 .483 2.072 2.188 2.067 2.245 1.358 80 498 2.175 .93 110 2160 8230 20 31 24 35 0 5183 146 5038 1.726 5343 5198 .579 1.824 .788 .867
2 3067 5225 342 172 2725 5053 3382 5662 353 187 3040 5490 0 0 1122 2296 98 100 100 100 100 100 7778 8530 .539 1.854 1.806 1.781 1.838 1.664 120 484 1.97 .93 120 2320 8230 20 32 40 52 0 4354 143 4211 1.545 4718 4575 .647 1.505 .628 .59
3 2938 4301 336 163 2602 4138 2947 4366 344 177 2611 4203 0 0 953 1294 79 96 100 100 100 100 6740 6814 .629 1.59 1.61 1.614 1.61 1.526 80 425 1.63 .91 110 2480 8220 19 30 56 67 0 3584 136 3448 1.325 3638 3503 .755 1.341 .406 .424
4 4429 6471 331 168 4098 6303 4568 6447 349 192 4237 6279 0 0 1260 2293 96 128 100 100 100 100 10401 10516 .65 1.538 1.482 1.517 1.49 1.566 80 446 1.653 .91 110 2640 8220 19 30 72 83 0 5393 140 5253 1.282 5373 5233 .78 1.235 .358 .304
5 1467 1381 324 173 1143 1208 1458 1340 339 190 1134 1167 0 0 267 300 95 105 100 100 100 100 2351 2301 .946 1.057 1.029 1.054 1.046 1.334 80 420 1.042 .91 110 2790 8220 19 30 87 98 0 1151 144 1007 .881 1117 973 1.135 .858 -.183 -.222
6 2840 9432 333 185 2507 9247 2851 10058 345 214 2518 9873 0 0 688 2792 83 144 100 100 100 100 11754 12391 .271 3.688 3.921 3.636 3.552 1.304 80 417 3.798 .95 110 2950 8230 20 31 103 114 0 7860 154 7706 3.074 8382 8228 .325 3.267 1.62 1.708
7 4339 9450 356 206 3983 9244 4613 10198 394 283 4257 9992 0 0 1178 2645 178 268 100 100 100 100 13227 14249 .431 2.321 2.347 2.318 2.27 1.249 80 431 2.323 .96 110 3110 8230 20 31 119 130 0 7875 172 7703 1.934 8498 8327 .517 1.956 .952 .968
8 2254 3074 372 205 1882 2869 2194 3178 410 280 1822 2973 0 0 484 844 178 260 100 100 100 100 4751 4795 .656 1.524 1.632 1.5 1.521 1.366 80 443 1.558 .94 110 3280 8220 19 30 136 147 0 2562 171 2391 1.27 2648 2478 .787 1.36 .345 .443
9 1793 2744 383 202 1410 2542 1809 2756 398 242 1426 2554 0 0 591 791 99 147 96 100 93 97 3952 3980 .555 1.803 1.791 1.752 1.645 1.697 80 391 1.716 .84 110 3430 8230 20 31 151 162 0 2287 168 2118 1.502 2297 2128 .666 1.493 .587 .578
10 6780 6096 398 194 6382 5902 7478 6501 406 208 7080 6307 0 0 2894 2286 81 79 97 100 97 100 12284 13387 1.081 .925 .891 .936 .851 1.621 80 409 .899 .91 110 3590 8220 19 30 167 178 0 5080 162 4918 .771 5418 5256 1.298 .742 -.376 -.43
11 4065 4518 443 220 3622 4298 4175 4684 479 236 3732 4464 0 0 1105 1332 256 103 98 100 98 100 7920 8196 .843 1.187 1.196 1.202 1.108 1.615 80 456 1.155 .93 110 3740 8230 20 31 182 193 0 3765 183 3582 .989 3903 3720 1.011 .997 -.016 -.005
12 4453 4617 451 202 4002 4415 4617 4833 464 228 4166 4631 0 0 1233 1461 116 110 98 100 98 100 8417 8797 .906 1.103 1.112 1.089 1.075 1.646 80 422 1.076 .91 110 3900 8230 20 31 198 209 0 3848 168 3679 .919 4028 3859 1.088 .926 -.121 -.11
13 2418 2873 439 203 1979 2670 2447 2893 456 268 2008 2690 0 0 516 769 109 165 98 100 97 98 4649 4698 .741 1.349 1.34 1.31 1.352 1.546 80 355 1.347 .89 100 4060 8230 21 31 215 225 0 2394 169 2225 1.124 2411 2242 .889 1.116 .169 .159
14 16379 19710 416 227 15963 19483 18505 21200 429 316 18089 20973 0 0 6580 7001 134 198 100 100 100 100 35446 39062 .819 1.221 1.159 1.295 1.206 1.703 80 406 1.219 .93 110 4210 8230 20 31 229 240 0 16425 189 16236 1.017 17667 17478 .983 .966 .024 -.05
15 5705 5309 367 230 5338 5079 5970 5163 386 303 5603 4933 0 0 1377 1426 133 182 100 100 100 100 10417 10536 1.051 .951 .88 .95 .931 1.352 80 345 .956 .92 100 4370 8220 20 30 246 256 0 4424 192 4233 .793 4303 4111 1.261 .734 -.335 -.447
16 3944 18528 335 181 3609 18347 4495 20932 341 212 4160 20751 0 0 1913 9954 66 108 100 100 100 100 21956 24911 .197 5.084 4.988 5.055 4.951 1.571 120 443 5.345 .96 120 4520 8230 20 32 260 272 0 15440 151 15289 4.236 17443 17293 .236 4.157 2.083 2.055
17 5459 6617 319 166 5140 6451 5531 6924 328 173 5212 6758 0 0 1334 1741 83 63 100 100 100 100 11591 11970 .797 1.255 1.297 1.251 1.198 1.288 80 380 1.286 .95 110 4680 8220 19 30 276 287 0 5514 138 5376 1.046 5770 5632 .956 1.081 .065 .112
18 3209 2157 312 167 2897 1990 3198 2146 333 178 2886 1979 0 0 844 644 118 106 100 100 100 100 4887 4865 1.456 .687 .686 .679 .661 1.453 80 430 .665 .93 110 4830 8220 19 30 291 302 0 1798 139 1658 .572 1788 1649 1.747 .571 -.805 -.807
19 1674 862 318 159 1356 703 1591 1026 345 183 1273 867 0 0 373 405 143 114 100 91 100 83 2059 2140 1.929 .518 .681 .421 .497 1.909 12 104 .578 .79 50 4970 8230 23 28 308 313 0 718 133 586 .432 855 723 2.315 .568 -1.211 -.817
20 3999 5300 328 167 3671 5133 4429 5626 330 172 4101 5459 0 0 1658 1757 79 69 98 100 98 100 8804 9560 .715 1.398 1.331 1.48 1.347 1.585 80 476 1.351 .92 110 5150 8230 20 31 323 334 0 4417 139 4278 1.165 4688 4549 .858 1.109 .221 .15

Total number of rows: 37632

Table truncated, full table size 8790 Kbytes.




Supplementary data files not provided
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