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Sample GSM91731 Query DataSets for GSM91731
Status Public on Jan 11, 2006
Title "088 Day3-2 in-vivo SP Inf, PBMC 2nd TC"
Sample type RNA
 
Channel 1
Source name "CRG, 1 round of amplification, Addie and Kate from 7/19/01"
Organism Homo sapiens
Characteristics "CRG, 1 round of amplification, Addie and Kate from 7/19/01"
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name "088 Day3-2 in-vivo SP Inf, PBMC 2nd TC"
Organism Homo sapiens
Characteristics "088 Day3-2 in-vivo SP Inf, PBMC 2nd TC"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19450.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 Jan 10, 2006
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 GPL3346
Series (1)
GSE4013 Host response to smallpox

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 3395 4444 269 899 3126 3545 3520 4307 271 905 3251 3408 0 0 1244 1851 67 210 98 100 98 97 6671 6659 .882 1.134 1.048 1.044 1.124 1.745 80 409 1.246 .91 100 1690 9000 91 101 88 98 0 4400 890 3510 1.123 4264 3374 .891 1.038 .167 .054
2 2058 6806 284 981 1774 5825 2071 6854 333 1150 1787 5873 0 0 444 1411 560 1721 100 100 94 94 7599 7660 .305 3.284 3.287 3.295 3.308 1.256 52 323 3.74 .9 90 1840 9000 91 100 103 112 0 6739 971 5767 3.251 6786 5815 .308 3.254 1.701 1.702
3 5162 11682 293 1062 4869 10620 5224 11682 330 1169 4931 10620 0 0 1487 3346 535 1585 100 100 100 98 15489 15551 .458 2.181 2.154 2.183 2.208 1.387 52 326 2.273 .94 90 2000 8990 90 99 119 128 0 11566 1051 10515 2.16 11566 10515 .463 2.132 1.111 1.092
4 9320 9043 291 1075 9029 7968 10065 8907 295 1112 9774 7832 0 0 3308 2786 65 252 100 100 98 100 16997 17606 1.133 .882 .801 .952 .87 1.69 80 432 .854 .94 110 2160 9000 90 101 134 145 0 8953 1064 7889 .874 8819 7754 1.144 .793 -.195 -.334
5 4597 10461 294 1078 4303 9383 4452 10280 305 1107 4158 9202 0 0 2324 5273 73 247 100 100 100 100 13686 13360 .459 2.181 2.213 2.179 2.283 1.595 80 383 2.281 .95 100 2320 9000 91 101 151 161 0 10357 1067 9290 2.159 10178 9111 .463 2.191 1.11 1.132
6 46456 29614 319 1081 46137 28533 44408 29863 336 1083 44089 28782 5 0 14177 12957 102 242 100 100 100 100 74670 72871 1.617 .618 .653 .564 .643 1.715 80 459 .65 .95 110 2480 9000 90 101 166 177 0 29321 1070 28250 .612 29567 28497 1.633 .646 -.708 -.63
7 1886 4187 329 1070 1557 3117 1995 3708 330 1087 1666 2638 0 0 1071 2272 86 286 96 84 90 81 4674 4304 .5 2.002 1.583 1.938 2.081 1.966 32 164 2.191 .93 60 2630 9000 93 99 184 190 0 4146 1059 3086 1.982 3671 2612 .505 1.568 .987 .649
8 7713 13465 305 1071 7408 12394 8366 13492 324 1105 8061 12421 0 0 2654 4378 105 316 100 100 98 100 19802 20482 .598 1.673 1.541 1.773 1.693 1.684 80 409 1.694 .95 100 2780 9000 91 101 197 207 0 13332 1060 12271 1.656 13358 12298 .604 1.526 .728 .609
9 2059 9719 301 1055 1758 8664 2162 9923 317 1100 1861 8868 0 0 672 3096 100 318 98 100 97 100 10422 10729 .203 4.928 4.765 5.2 4.834 1.601 80 404 5.088 .94 110 2940 9010 91 102 212 223 0 9623 1045 8578 4.88 9825 8780 .205 4.718 2.287 2.238
10 5010 16397 302 1062 4708 15335 5252 16928 312 1087 4950 15866 0 0 1805 5507 73 238 100 100 100 100 20043 20816 .307 3.257 3.205 3.279 3.263 1.437 52 316 3.443 .93 90 3090 8990 90 99 228 237 0 16235 1051 15183 3.225 16760 15709 .31 3.174 1.689 1.666
11 2432 6844 303 1019 2129 5825 2483 6852 315 1046 2180 5833 0 0 948 2458 77 246 100 100 98 100 7954 8013 .365 2.736 2.676 2.821 2.772 1.53 80 377 2.823 .93 100 3250 9000 91 101 244 254 0 6776 1009 5767 2.709 6784 5775 .369 2.649 1.438 1.406
12 3486 10447 313 1016 3173 9431 3660 10615 354 1102 3347 9599 0 0 1232 3413 246 567 100 100 98 100 12604 12946 .336 2.972 2.868 3.076 3.104 1.602 52 312 3.052 .94 90 3390 8990 90 99 258 267 0 10344 1006 9338 2.943 10510 9504 .34 2.84 1.557 1.506
13 3274 9652 317 1014 2957 8638 3197 10053 349 1100 2880 9039 0 0 1064 3173 237 555 100 100 100 100 11595 11919 .342 2.921 3.139 2.864 2.917 1.45 52 333 3.128 .93 90 3560 8980 89 98 275 284 0 9556 1004 8552 2.892 9953 8950 .346 3.107 1.532 1.636
14 6805 17661 314 1076 6491 16585 6979 17785 319 1100 6665 16709 0 0 2200 5760 69 245 100 100 100 100 23076 23374 .391 2.555 2.507 2.511 2.517 1.375 80 430 2.662 .96 110 3720 8990 89 100 290 301 0 17486 1065 16421 2.53 17609 16544 .395 2.482 1.339 1.312
15 3602 11005 311 1129 3291 9876 3469 10938 313 1155 3158 9809 0 0 1486 3889 68 246 100 100 100 100 13167 12967 .333 3.001 3.106 3.111 2.955 1.47 80 353 3.041 .94 100 3870 9000 91 101 306 316 0 10896 1118 9778 2.971 10830 9712 .337 3.075 1.571 1.621
16 8616 30677 322 1158 8294 29519 9245 33401 328 1172 8923 32243 0 0 2264 9114 70 236 100 100 100 100 37813 41166 .281 3.559 3.613 3.503 3.598 1.37 80 356 3.708 .97 100 4030 9000 91 101 322 332 0 30373 1147 29227 3.524 33070 31924 .284 3.578 1.817 1.839
17 2484 6879 336 1161 2148 5718 2343 6508 334 1170 2007 5347 0 0 979 2453 71 243 100 100 100 100 7866 7354 .376 2.662 2.664 2.737 2.669 1.488 80 378 2.723 .95 100 4180 9000 91 101 337 347 0 6811 1150 5661 2.636 6444 5294 .379 2.638 1.398 1.399
18 1664 4303 330 1116 1334 3187 1798 4535 341 1134 1468 3419 0 0 483 1138 80 238 100 100 100 100 4521 4887 .419 2.389 2.329 2.398 2.403 1.415 32 165 2.505 .93 60 4330 9000 93 99 354 360 0 4260 1105 3155 2.365 4490 3385 .423 2.306 1.242 1.205
19 2785 13574 321 1121 2464 12453 2845 14077 329 1140 2524 12956 0 0 694 2944 75 240 100 100 100 100 14917 15480 .198 5.054 5.133 5.228 4.957 1.457 80 399 5.148 .95 100 4490 9000 91 101 368 378 0 13440 1110 12330 5.004 13938 12828 .2 5.082 2.323 2.345
20 1236 3362 310 1119 926 2243 1299 3606 320 1139 989 2487 0 0 288 847 78 246 98 97 97 93 3169 3476 .413 2.422 2.515 2.309 2.393 1.774 80 358 2.647 .9 100 4650 9000 91 101 384 394 0 3329 1108 2221 2.398 3570 2462 .417 2.49 1.262 1.316

Total number of rows: 37632

Table truncated, full table size 8644 Kbytes.




Supplementary data files not provided
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