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Sample GSM91154 Query DataSets for GSM91154
Status Public on Jan 07, 2006
Title Bs+LLO_vs_Bs-LLO_T1_R1
Sample type RNA
 
Channel 1
Source name experimental sample
Organism Mus musculus
Characteristics experimental sample
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name experimental sample
Organism Mus musculus
Characteristics experimental sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25466.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 06, 2006
Last update date Sep 22, 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 GPL3328
Series (1)
GSE3991 Listeria host responses

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 1137 625 580 310 557 315 403 167 592 333 -177 -143 0 0 1339 717 86 119 36 36 32 36 872 -320 1.768 .566 null .666 .633 2.318 52 279 .402 .61 80 2090 7630 75 83 69 77 0 718 356 362 .65 192 null 1.538 null -.621 null
2 6534 7076 590 312 5944 6764 1042 1310 613 336 452 998 0 0 9953 8812 217 122 55 67 50 63 12708 1450 .879 1.138 2.208 .52 .707 4.35 52 280 .963 .7 90 2240 7620 73 82 83 92 0 8133 359 7775 1.308 1506 1147 .765 2.538 .387 1.344
3 4601 3250 566 311 4035 2939 2322 1908 652 401 1756 1597 0 0 4588 3389 1148 900 52 51 48 47 6974 3353 1.373 .728 .909 .661 .761 4.028 80 431 .695 .68 110 2360 7620 72 83 94 105 0 3736 357 3378 .837 2193 1836 1.194 1.045 -.256 .064
4 1162 707 575 308 587 399 619 239 575 314 44 -69 0 0 1205 808 79 71 48 40 46 38 986 -25 1.471 .68 null .559 .621 2.501 52 232 .569 .67 80 2520 7630 75 83 112 120 0 813 354 459 .781 275 null 1.28 null -.356 null
5 1579 994 599 320 980 674 1425 469 612 324 826 149 0 0 1335 990 105 72 57 53 55 50 1654 975 1.454 .688 .18 .67 .734 2.966 52 225 .626 .65 80 2640 7630 75 83 124 132 0 1143 368 775 .791 539 171 1.265 .207 -.339 -2.27
6 22665 19153 601 325 22064 18828 16139 11323 626 356 15538 10998 1 0 22045 19311 193 491 78 75 76 66 40892 26536 1.172 .853 .708 .515 .83 6.968 80 453 .869 .75 110 2790 7620 72 83 137 148 0 22015 374 21641 .981 13015 12641 1.02 .814 -.028 -.298
7 2180 1416 632 330 1548 1086 689 447 667 378 57 117 0 0 2722 2114 198 280 46 40 44 34 2634 174 1.425 .702 2.053 .574 .607 2.58 52 303 .672 .68 80 2960 7630 75 83 156 164 0 1628 379 1248 .806 514 134 1.24 2.359 -.31 1.238
8 3175 2257 639 337 2536 1920 1446 1024 702 421 807 687 0 0 3484 2718 239 337 65 56 59 50 4456 1494 1.321 .757 .851 .639 .618 4.025 32 170 .697 .57 60 3110 7630 76 82 172 178 0 2594 387 2207 .87 1177 790 1.149 .979 -.201 -.031
9 8234 6669 628 322 7606 6347 1699 1215 694 341 1071 893 0 0 10902 10560 406 122 53 68 53 62 13953 1964 1.198 .834 .834 .497 .619 4.359 32 220 .89 .54 70 3250 7630 75 82 185 192 0 7666 370 7295 .959 1397 1026 1.043 .958 -.06 -.061
10 2860 2354 671 320 2189 2034 698 568 751 426 27 248 0 0 5044 4340 674 861 30 28 26 25 4223 275 1.076 .929 9.185 .671 .666 3.189 52 309 .797 .62 80 3400 7630 75 83 200 208 0 2706 368 2338 1.068 653 285 .936 10.558 .095 3.4
11 5427 4726 786 340 4641 4386 2472 2524 1049 590 1686 2184 0 0 5164 4600 1212 1391 50 66 41 41 9027 3870 1.058 .945 1.295 1.141 .824 4.737 12 98 1.003 .34 50 3560 7620 75 80 217 222 0 5432 391 5041 1.086 2901 2510 .921 1.489 .119 .574
12 1106 524 762 318 344 206 676 246 1508 1420 -86 -72 0 0 989 562 5812 7022 0 0 0 0 550 -158 1.67 .599 null .744 .732 3.457 52 271 6.475 .64 80 3690 7630 75 83 229 237 0 602 366 237 .688 283 null 1.453 null -.539 null
13 1123 521 832 332 291 189 778 296 1814 1749 -54 -36 0 0 763 598 6578 7951 0 0 0 0 480 -90 1.54 .649 null .701 .828 3.24 52 210 9.617 .16 80 3840 7630 75 83 244 252 0 599 382 217 .747 340 null 1.34 null -.422 null
14 4644 4858 975 341 3669 4517 4230 3938 1166 389 3255 3597 0 0 2957 3379 2236 435 62 85 38 80 8186 6852 .812 1.231 1.105 1.307 1.209 4.005 120 456 .746 .52 120 3960 7630 73 85 254 266 0 5584 392 5192 1.415 4526 4134 .707 1.27 .501 .345
15 21924 17104 1056 345 20868 16759 10447 6918 1344 514 9391 6573 6 0 23118 19265 2665 1066 67 77 56 71 37627 15964 1.245 .803 .7 .656 .705 4.473 80 423 .787 .81 100 4120 7620 73 83 271 281 0 19660 397 19263 .923 7952 7555 1.083 .805 -.115 -.314
16 11528 9240 905 338 10623 8902 10495 7670 1718 982 9590 7332 0 0 8844 6454 3011 2053 75 83 66 75 19525 16922 1.193 .838 .765 .993 .644 7.613 12 98 .637 .47 50 4290 7620 75 80 290 295 0 10621 389 10232 .963 8816 8428 1.038 .879 -.054 -.186
17 1610 646 845 325 765 321 1021 277 1386 409 176 -48 0 0 1517 929 4173 426 7 15 0 15 1086 128 2.383 .42 null .719 .959 4.283 52 259 .076 .45 80 4420 7630 75 83 302 310 0 743 374 369 .482 318 null 2.073 null -1.052 null
18 11381 9639 776 331 10605 9308 2833 2102 826 358 2057 1771 0 0 16687 16051 232 142 68 78 65 71 19913 3828 1.139 .878 .861 .739 .699 5.309 32 164 .979 .58 60 4570 7630 76 82 318 324 0 11079 380 10699 1.009 2416 2036 .991 .99 .013 -.015
19 989 658 664 316 325 342 601 326 684 327 -63 10 0 0 978 732 140 81 28 38 23 30 667 -53 .95 1.052 null .91 .633 2.998 52 248 .566 .51 80 4710 7630 75 83 331 339 0 756 363 393 1.21 375 11 .827 null .274 null
20 5919 5578 756 317 5163 5261 1524 1556 838 325 768 1239 0 0 9429 9201 395 79 67 73 48 73 10424 2007 .981 1.019 1.613 1.021 .845 3.761 52 278 .977 .6 90 4850 7630 74 83 344 353 0 6411 364 6047 1.171 1789 1424 .854 1.854 .228 .891

Total number of rows: 42624

Table truncated, full table size 9713 Kbytes.




Supplementary data files not provided
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