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Sample GSM84930 Query DataSets for GSM84930
Status Public on Nov 23, 2005
Title s9146, p717, 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 s9146, p717, Pax whole blood
Organism Homo sapiens
Characteristics s9146, p717, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22930.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
1 480 561 191 180 289 381 461 549 194 195 270 369 0 0 153 208 53 76 93 93 84 87 670 639 .759 1.318 1.367 1.303 1.379 1.514 32 195 1.4 .88 70 2460 9070 27 34 70 77 0 623 200 423 1.465 610 410 .683 1.519 .551 .603
2 530 838 186 194 344 644 520 810 192 213 334 616 0 0 155 232 58 104 97 100 91 98 988 950 .534 1.872 1.844 2.034 1.815 1.784 80 420 1.901 .88 100 2640 9070 26 36 87 97 0 931 216 716 2.08 900 684 .481 2.049 1.057 1.035
3 488 1435 183 237 305 1198 437 1278 186 261 254 1041 0 0 209 684 50 119 92 100 80 100 1503 1295 .255 3.928 4.098 4.55 3.916 1.784 52 244 4.021 .91 80 2790 9080 28 36 103 111 0 1594 263 1331 4.364 1420 1157 .229 4.554 2.126 2.187
4 366 487 181 252 185 235 376 476 188 271 195 224 0 0 123 165 65 129 77 70 63 43 420 419 .787 1.27 1.149 1.21 1.208 2.302 80 467 1.543 .72 100 2950 9060 25 35 118 128 0 541 280 261 1.411 529 249 .709 1.276 .497 .352
5 574 640 180 226 394 414 563 654 200 245 383 428 0 0 117 127 84 115 100 100 100 96 808 811 .952 1.051 1.117 1.046 1.067 1.331 32 176 1.163 .89 60 3110 9090 30 36 136 142 0 711 251 460 1.168 727 476 .857 1.242 .223 .312
6 502 1315 199 206 303 1109 492 1330 212 228 293 1124 0 0 133 380 78 112 96 100 86 100 1412 1417 .273 3.66 3.836 3.871 3.51 1.641 52 363 4.04 .8 90 3260 9060 25 34 149 158 0 1461 229 1232 4.067 1478 1249 .246 4.262 2.024 2.092
7 838 1425 185 230 653 1195 893 1413 197 262 708 1183 0 0 184 208 78 131 98 100 96 100 1848 1891 .546 1.83 1.671 1.952 1.63 1.741 52 351 1.818 .89 90 3420 9050 24 33 165 174 0 1583 256 1328 2.033 1570 1314 .492 1.857 1.024 .893
8 454 536 208 229 246 307 438 542 215 261 230 313 0 0 99 133 70 122 98 90 84 67 553 543 .801 1.248 1.361 1.2 1.213 1.675 52 298 1.32 .76 90 3580 9090 28 37 181 190 0 596 254 341 1.387 602 348 .721 1.512 .472 .597
9 592 746 184 175 408 571 564 702 191 197 380 527 0 0 253 235 55 106 93 100 92 100 979 907 .715 1.4 1.387 1.325 1.304 1.574 80 506 1.454 .81 110 3740 9050 23 34 196 207 0 829 194 634 1.555 780 586 .643 1.541 .637 .624
10 517 574 175 165 342 409 516 571 178 170 341 406 0 0 155 184 47 58 96 100 90 94 751 747 .836 1.196 1.191 1.296 1.152 1.83 52 311 1.204 .82 90 3880 9060 25 34 211 220 0 638 183 454 1.329 634 451 .753 1.323 .41 .404
11 538 718 160 155 378 563 516 671 166 162 356 516 0 0 188 249 48 57 92 100 92 100 941 872 .671 1.489 1.449 1.551 1.354 2.098 80 416 1.521 .85 100 4040 9050 24 34 227 237 0 798 172 626 1.655 746 573 .604 1.61 .727 .687
12 426 429 158 163 268 266 416 426 166 170 258 263 0 0 189 134 44 61 87 87 84 84 534 521 1.008 .993 1.019 1.047 1.004 1.746 32 210 .96 .81 70 4180 9050 25 32 242 249 0 477 181 296 1.103 473 292 .907 1.133 .141 .18
13 537 668 152 159 385 509 483 580 159 171 331 421 0 0 167 279 41 58 98 100 98 100 894 752 .756 1.322 1.272 1.306 1.229 1.654 52 344 1.47 .88 90 4350 9050 24 33 258 267 0 742 177 566 1.469 644 468 .681 1.413 .555 .499
14 1603 1255 159 179 1444 1076 1772 1244 181 201 1613 1065 0 0 803 506 67 86 92 100 92 97 2520 2678 1.342 .745 .66 .789 .68 1.885 80 411 .682 .92 100 4510 9060 25 35 274 284 0 1394 199 1196 .828 1382 1183 1.208 .734 -.272 -.447
15 581 752 177 232 404 520 596 723 202 259 419 491 0 0 132 214 89 124 93 100 93 93 924 910 .777 1.287 1.172 1.347 1.14 2.076 32 203 1.319 .81 70 4640 9050 25 32 288 295 0 836 258 578 1.43 803 546 .699 1.302 .516 .381
16 999 4447 168 231 831 4216 1051 4601 191 340 883 4370 0 0 320 1139 77 252 93 100 92 100 5047 5253 .197 5.073 4.949 4.93 4.647 1.352 80 424 4.949 .94 100 4820 9050 24 34 305 315 0 4941 257 4684 5.637 5112 4856 .177 5.499 2.495 2.459
17 1014 709 173 172 841 537 1007 682 186 248 834 510 0 0 270 163 63 187 100 100 100 86 1378 1344 1.566 .639 .612 .644 .629 1.321 52 311 .6 .83 90 4960 9050 24 33 319 328 0 788 191 597 .709 758 567 1.409 .679 -.495 -.558
18 872 1364 177 170 695 1194 929 1423 186 185 752 1253 0 0 234 373 52 84 98 100 98 100 1889 2005 .582 1.718 1.666 1.72 1.654 1.328 80 412 1.742 .94 100 5130 9060 25 35 336 346 0 1516 189 1327 1.909 1581 1392 .524 1.851 .933 .889
19 206 166 162 146 44 20 158 135 165 154 -4 -11 0 0 139 83 34 50 27 20 16 13 64 -15 2.2 .455 null .892 .872 2.91 80 393 .608 .61 100 5290 9050 24 34 352 362 -50 184 162 22 .505 150 null 1.98 null -.986 null
20 697 533 156 148 541 385 707 553 159 155 551 405 0 0 277 183 29 47 96 96 94 90 926 956 1.405 .712 .735 .728 .663 1.912 52 261 .665 .9 80 5450 9050 25 33 369 377 0 592 164 428 .791 614 450 1.265 .817 -.339 -.292

Total number of rows: 37632

Table truncated, full table size 8216 Kbytes.




Supplementary data files not provided
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