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Sample GSM82126 Query DataSets for GSM82126
Status Public on Nov 05, 2005
Title actA T120 parallel
Sample type RNA
 
Channel 1
Source name CRE reference pool
Organism Homo sapiens
Characteristics CRE reference pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name experimental sample
Organism Homo sapiens
Characteristics experimental sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12853.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 Nov 04, 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 GPL2868
Series (1)
GSE3567 Listeria infection of Caco-2 cells

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 3637 3851 398 452 3239 3399 3314 3640 524 552 2916 3188 0 0 2319 2281 665 652 88 87 71 76 6638 6104 .953 1.049 1.093 1.139 1.054 1.763 80 372 1.016 .94 100 1890 19080 91 101 84 94 0 7879 925 6954 2.147 7447 6522 .466 2.237 1.102 1.161
2 7595 4228 414 461 7181 3767 6982 4181 603 629 6568 3720 0 0 5013 2305 730 722 90 90 85 75 10948 10288 1.906 .525 .566 .596 .588 1.664 80 344 .48 .89 100 2040 19080 91 101 99 109 0 8650 943 7707 1.073 8554 7611 .932 1.159 .102 .213
3 4018 3447 419 444 3599 3003 3984 3347 484 500 3565 2903 0 0 2013 1690 298 255 100 100 95 100 6602 6468 1.198 .834 .814 .857 .895 1.532 80 350 .82 .94 100 2200 19080 91 101 115 125 0 7052 908 6144 1.707 6847 5939 .586 1.666 .772 .736
4 2915 788 412 441 2503 347 2674 723 430 451 2262 282 0 0 1498 241 166 83 100 90 98 73 2850 2544 7.213 .139 .125 .135 .121 2.901 80 335 .078 .46 100 2350 19080 91 101 130 140 0 1612 902 710 .284 1479 577 3.526 .255 -1.818 -1.971
5 8720 3890 411 451 8309 3439 7383 3621 422 460 6972 3170 0 0 5371 1894 84 74 100 100 100 100 11748 10142 2.416 .414 .455 .45 .439 1.388 80 363 .377 .96 100 2500 19080 91 101 145 155 0 7958 923 7036 .847 7408 6485 1.181 .93 -.24 -.104
6 5846 5006 433 479 5413 4527 5497 4709 439 494 5064 4230 0 0 3536 2899 87 86 100 100 100 100 9940 9294 1.196 .836 .835 .835 .826 1.792 80 363 .809 .91 100 2650 19080 91 101 160 170 0 10242 980 9262 1.711 9634 8654 .584 1.709 .775 .773
7 3437 2953 430 478 3007 2475 3202 2619 433 493 2772 2141 0 0 1343 1132 85 95 100 100 100 100 5482 4913 1.215 .823 .772 .828 .838 1.44 52 326 .817 .93 90 2800 19070 90 99 175 184 0 6041 978 5063 1.684 5358 4380 .594 1.58 .752 .66
8 4288 4895 449 507 3839 4388 3679 4215 541 673 3230 3708 0 0 2384 2670 327 423 100 98 100 96 8227 6938 .875 1.143 1.148 1.111 1.118 1.802 80 463 1.138 .9 110 2960 19070 89 100 190 201 0 10014 1037 8977 2.338 8623 7586 .428 2.349 1.226 1.232
9 37435 21412 572 747 36863 20665 36188 19247 745 938 35616 18500 7 0 15643 11478 527 609 100 100 100 100 57528 54116 1.784 .561 .519 .517 .538 1.69 52 342 .556 .89 90 3100 19070 90 99 205 214 0 43806 1528 42277 1.147 39376 37848 .872 1.063 .198 .088
10 3584 1188 665 710 2919 478 3686 1153 812 791 3021 443 0 0 564 276 492 352 100 58 100 16 3397 3464 6.107 .164 .147 .145 .163 1.637 12 104 .216 .46 50 3260 19060 91 96 223 228 0 2430 1453 978 .335 2359 906 2.985 .3 -1.578 -1.737
11 3907 1111 460 518 3447 593 3811 1064 531 615 3351 546 0 0 1478 301 314 261 100 82 100 53 4040 3897 5.813 .172 .163 .159 .158 2.213 52 321 .125 .64 90 3400 19070 90 99 235 244 0 2273 1060 1213 .352 2177 1117 2.841 .333 -1.507 -1.585
12 8145 19582 413 471 7732 19111 8122 18512 433 498 7709 18041 0 0 4531 10872 143 107 100 100 100 100 26843 25750 .405 2.472 2.34 2.562 2.463 1.894 80 396 2.704 .88 110 3550 19070 89 100 249 260 0 40062 964 39098 5.057 37873 36909 .198 4.788 2.338 2.259
13 8991 4986 418 471 8573 4515 8686 4990 422 481 8268 4519 0 0 6156 3055 76 71 100 100 100 100 13088 12787 1.899 .527 .547 .544 .51 2.009 80 342 .488 .92 100 3690 19070 90 100 264 274 0 10201 964 9237 1.077 10209 9245 .928 1.118 .108 .161
14 35790 26393 413 466 35377 25927 36634 25456 419 467 36221 24990 17 2 21929 18180 75 69 100 100 100 100 61304 61211 1.364 .733 .69 .655 .782 2.008 80 431 .75 .93 110 3850 19070 89 100 279 290 0 53996 953 53043 1.499 52079 51126 .667 1.411 .584 .497
15 3192 2174 406 467 2786 1707 2352 1661 447 489 1946 1194 0 0 1928 1236 328 160 97 97 93 92 4493 3140 1.632 .613 .614 .591 .637 1.759 80 353 .604 .94 100 3990 19070 90 100 294 304 0 4448 955 3492 1.254 3398 2443 .798 1.255 .326 .328
16 9762 7525 429 492 9333 7033 8400 6752 489 536 7971 6260 0 0 4921 3971 347 200 100 100 100 100 16366 14231 1.327 .754 .785 .72 .735 1.48 80 381 .756 .94 110 4150 19070 89 100 309 320 0 15395 1007 14388 1.542 13814 12807 .649 1.607 .624 .684
17 21547 30381 440 504 21107 29877 21313 29365 473 527 20873 28861 0 0 12578 16484 174 140 100 100 100 100 50984 49734 .706 1.416 1.383 1.49 1.52 1.749 80 435 1.43 .9 110 4300 19070 89 100 324 335 0 62155 1031 61124 2.896 60076 59045 .345 2.829 1.534 1.5
18 1698 922 433 488 1265 434 1661 878 439 488 1228 390 0 0 313 226 82 69 100 96 100 96 1699 1618 2.915 .343 .318 .305 .311 1.923 32 200 .309 .68 70 4450 19050 89 96 341 348 0 1886 998 888 .702 1796 798 1.425 .65 -.511 -.622
19 20473 19041 419 460 20054 18581 19479 16759 421 469 19060 16299 0 0 10827 10451 81 77 100 100 100 100 38635 35359 1.079 .927 .855 .924 .966 1.483 80 442 .923 .92 110 4590 19070 89 100 353 364 0 38955 941 38014 1.896 34286 33345 .528 1.749 .923 .807
20 5514 4093 415 469 5099 3624 4959 3735 417 477 4544 3266 0 0 3088 2221 84 83 100 100 100 98 8723 7810 1.407 .711 .719 .674 .774 1.886 80 369 .694 .93 100 4740 19070 90 100 369 379 0 8374 960 7414 1.454 7641 6682 .688 1.47 .54 .556

Total number of rows: 24192

Table truncated, full table size 5503 Kbytes.




Supplementary data files not provided
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