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Sample GSM63321 Query DataSets for GSM63321
Status Public on Jul 09, 2005
Title Human Malaria __raw_14
Sample type RNA
 
Channel 1
Source name reference
Organism Homo sapiens
Characteristics Stratagene, amplified with Ambion method
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name clinical sample
Organism Homo sapiens
Characteristics 3_Convalescent, follow-up to #23; PAXgene sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37522.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jul 08, 2005
Last update date Nov 16, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2614
Series (1)
GSE2900 Host Response Malaria

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 535 575 97 269 438 306 532 537 101 285 435 268 0 0 288 222 26 119 90 78 90 59 744 703 1.431 .699 .616 .733 .727 2.057 32 223 .746 .74 70 1880 6880 41 48 77 84 0 529 247 281 .642 494 246 1.556 .567 -.638 -.82 -.82
2 685 898 102 281 583 617 738 909 123 307 636 628 0 0 274 311 79 162 96 90 93 78 1200 1264 .945 1.058 .987 1.001 1.032 1.638 32 168 1.104 .86 60 2020 6900 44 50 92 98 0 826 258 567 .973 836 578 1.027 .908 -.039 -.139 -.139
3 604 577 99 257 505 320 557 526 101 265 458 269 0 0 382 263 24 101 92 78 84 57 825 727 1.578 .634 .587 .645 .614 2.725 52 284 .691 .8 80 2190 6890 42 50 108 116 0 531 236 294 .583 484 247 1.716 .54 -.779 -.889 -.889
4 343 546 97 248 246 298 355 564 98 261 258 316 0 0 131 196 21 105 98 82 96 69 544 574 .826 1.211 1.225 1.087 1.251 2.531 52 303 1.585 .73 90 2330 6860 38 47 121 130 0 502 228 274 1.114 519 291 .898 1.126 .156 .172 .172
5 367 462 95 259 272 203 388 437 101 271 293 178 0 0 150 180 26 116 93 68 93 34 475 471 1.34 .746 .608 .724 .827 2.176 32 166 1.143 .58 60 2470 6880 42 48 137 143 0 425 238 187 .686 402 164 1.457 .559 -.543 -.84 -.84
6 358 1024 99 275 259 749 354 993 113 293 255 718 0 0 129 417 80 132 95 100 73 92 1008 973 .346 2.892 2.816 2.822 2.857 1.61 80 506 3.372 .88 100 2640 6870 39 49 152 162 0 942 253 689 2.66 913 660 .376 2.589 1.411 1.373 1.373
7 1056 1313 106 277 950 1036 1388 1431 155 332 1282 1154 0 0 611 708 200 239 81 78 71 68 1986 2436 .917 1.091 .9 1.032 1.052 2.043 32 236 1.189 .91 70 2820 6900 43 50 171 178 0 1207 255 953 1.003 1316 1061 .997 .828 .004 -.273 -.273
8 481 604 97 274 384 330 569 563 100 283 472 289 0 0 229 230 28 94 90 84 81 62 714 761 1.164 .859 .612 .872 .881 2.133 32 206 1.013 .78 70 2980 6890 42 49 187 194 0 555 252 303 .79 518 266 1.265 .563 -.339 -.829 -.829
9 511 1017 100 287 411 730 517 970 107 311 417 683 0 0 187 423 44 190 98 93 96 82 1141 1100 .563 1.776 1.638 1.723 1.763 1.671 80 479 2.401 .8 100 3110 6880 40 50 199 209 0 935 264 671 1.633 892 628 .612 1.506 .708 .591 .591
10 1234 2866 103 314 1131 2552 1331 3180 144 398 1228 2866 0 0 597 1363 164 392 93 96 93 90 3683 4094 .443 2.256 2.334 2.325 2.354 2.091 32 140 2.361 .94 60 3300 6880 42 48 220 226 0 2636 289 2347 2.075 2924 2636 .482 2.146 1.053 1.102 1.102
11 1025 2019 98 268 927 1751 1034 1920 129 339 936 1652 0 0 362 846 198 380 96 96 91 95 2678 2588 .529 1.889 1.765 1.863 1.758 1.49 80 434 2.062 .91 100 3420 6880 40 50 230 240 0 1857 246 1610 1.737 1766 1519 .576 1.623 .797 .699 .699
12 932 2026 110 282 822 1744 1069 2077 118 315 959 1795 0 0 571 1251 49 146 87 84 87 81 2566 2754 .471 2.122 1.872 2.194 2.167 1.932 32 147 2.193 .95 60 3590 6860 40 46 249 255 0 1863 259 1604 1.951 1910 1651 .513 1.721 .964 .784 .784
13 790 1137 121 317 669 820 761 1078 150 346 640 761 0 0 484 634 109 165 78 81 71 65 1489 1401 .816 1.226 1.189 .973 1.273 2.964 32 230 1.334 .89 70 3720 6900 43 50 261 268 0 1046 292 754 1.127 991 700 .887 1.094 .173 .129 .129
14 2351 1453 101 273 2250 1180 2306 1321 115 296 2205 1048 0 0 979 605 70 130 100 100 100 100 3430 3253 1.907 .524 .475 .518 .484 1.507 80 516 .5 .89 110 3890 6870 38 49 276 287 0 1336 251 1085 .482 1215 964 2.073 .437 -1.052 -1.194 -1.194
15 746 1674 105 302 641 1372 729 1372 132 346 624 1070 0 0 498 1117 122 221 78 87 62 75 2013 1694 .467 2.14 1.715 2.669 2.198 2.57 32 172 2.36 .84 60 4050 6900 44 50 295 301 0 1539 278 1262 1.968 1262 984 .508 1.577 .977 .657 .657
16 1428 2485 103 285 1325 2200 1411 2337 112 308 1308 2052 0 0 504 824 57 164 98 100 98 98 3525 3360 .602 1.66 1.569 1.678 1.67 1.503 80 519 1.712 .94 110 4220 6870 38 49 309 320 0 2285 262 2023 1.527 2149 1887 .655 1.443 .611 .529 .529
17 1207 705 96 262 1111 443 1174 711 99 282 1078 449 0 0 457 210 39 149 100 94 100 73 1554 1527 2.508 .399 .417 .372 .414 1.876 52 322 .372 .73 90 4370 6880 40 49 325 334 0 648 241 407 .367 654 413 2.727 .383 -1.447 -1.384 -1.384
18 398 1186 98 263 300 923 413 1056 103 280 315 793 0 0 250 819 28 122 76 78 69 71 1223 1108 .325 3.077 2.517 3.103 3.213 2.758 52 254 3.452 .9 80 4520 6900 43 51 341 349 0 1091 242 849 2.829 971 729 .353 2.315 1.501 1.211 1.211
19 194 300 98 274 96 26 106 288 106 313 8 14 0 0 234 118 124 398 18 1 13 0 122 22 3.692 .271 1.75 1.864 2.151 4.996 80 405 41.93 .07 100 4680 6890 41 51 356 366 -50 276 252 24 .249 265 13 4.015 1.609 -2.005 .686
20 654 500 98 284 556 216 665 502 99 350 567 218 0 0 294 170 18 617 96 0 96 0 772 785 2.574 .388 .384 .362 .447 2.399 32 156 .404 .64 60 4830 6870 41 47 373 379 0 460 261 199 .357 462 200 2.799 .354 -1.485 -1.5 -1.5

Total number of rows: 37632

Table truncated, full table size 8639 Kbytes.




Supplementary data files not provided
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