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Sample GSM81871 Query DataSets for GSM81871
Status Public on Nov 04, 2005
Title LT2 v SL1344 1
Sample type genomic
 
Channel 1
Source name SL1344
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics SL1344
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name LT2
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics LT2
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23956.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 03, 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 GPL3048
Series (1)
GSE3564 Genomic comparison of Salmonella enterica serovars and Salmonella bongori

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 7064 9952 695 701 6369 9251 6452 8169 715 690 5757 7468 0 0 4368 6921 209 214 100 100 100 100 15620 13225 .688 1.453 1.297 1.391 1.352 1.236 32 236 1.516 .99 70 1110 18430 63 70 55 62 0 6863 483 6380 1.002 5634 5150 .998 .895 .002 -.161
2 8131 11956 505 466 7626 11490 5165 7413 524 488 4660 6947 0 0 6561 10061 118 155 100 100 100 100 19116 11607 .664 1.507 1.491 1.458 1.473 1.22 52 340 1.528 .99 80 1340 18430 63 71 78 86 0 8246 321 7924 1.039 5112 4791 .962 1.028 .055 .04
3 3369 4763 509 477 2860 4286 2041 2721 524 499 1532 2244 0 0 3005 4631 93 114 96 90 90 90 7146 3776 .667 1.499 1.465 1.39 1.381 1.418 32 170 1.53 .99 60 1580 18420 63 69 103 109 0 3285 329 2956 1.034 1877 1548 .968 1.01 .048 .015
4 8509 10663 582 542 7927 10121 6000 7122 627 618 5418 6580 0 0 6057 8015 181 223 100 98 100 97 18048 11998 .783 1.277 1.214 1.213 1.237 1.443 80 650 1.298 .99 110 1790 18430 61 72 121 132 0 7354 374 6980 .881 4912 4538 1.136 .838 -.184 -.256
5 9309 10979 616 554 8693 10425 6663 8451 830 687 6047 7897 0 0 6214 6633 601 386 98 100 97 100 19118 13944 .834 1.199 1.306 1.262 1.261 1.341 80 650 1.155 .98 110 2010 18430 61 72 143 154 0 7572 382 7190 .827 5828 5446 1.209 .901 -.274 -.151
6 7328 10275 631 578 6697 9697 4723 5264 933 697 4092 4686 0 0 5990 9202 823 360 100 100 84 100 16394 8778 .691 1.448 1.145 1.41 1.418 1.275 52 420 1.502 .98 90 2230 18420 61 70 166 175 0 7086 399 6688 .999 3630 3232 1.001 .79 -.002 -.341
7 5869 8777 647 608 5222 8169 3015 3737 649 619 2368 3129 0 0 5080 8535 98 113 100 100 100 100 13391 5497 .639 1.564 1.321 1.469 1.518 1.257 52 332 1.639 .99 80 2460 18410 61 69 190 198 0 6053 419 5634 1.079 2577 2158 .927 .911 .11 -.134
8 7890 9657 718 730 7172 8927 4716 5696 773 789 3998 4966 0 0 7811 10373 245 257 92 91 83 82 16099 8964 .803 1.245 1.242 1.102 1.229 1.538 80 552 1.303 .99 100 2700 18410 60 70 213 223 0 6660 503 6157 .858 3928 3425 1.165 .857 -.22 -.223
9 11989 17204 676 655 11313 16549 10805 15298 703 695 10129 14643 0 0 5983 9432 167 185 100 100 100 100 27862 24772 .684 1.463 1.446 1.423 1.442 1.187 52 420 1.5 .99 90 2920 18410 60 69 235 244 0 11865 452 11413 1.009 10550 10099 .991 .997 .013 -.004
10 8480 12867 640 645 7840 12222 6363 8740 670 660 5723 8095 0 0 5781 10441 155 147 100 100 100 100 20062 13818 .641 1.559 1.414 1.438 1.492 1.296 52 412 1.686 .98 90 3140 18400 59 68 257 266 0 8874 445 8429 1.075 6028 5583 .93 .975 .105 -.036
11 1668 2244 583 576 1085 1668 893 1055 591 582 310 479 0 0 1587 2444 87 92 82 73 73 71 2753 789 .65 1.537 1.545 1.356 1.417 1.781 52 412 1.552 .97 90 3360 18400 59 68 279 288 -50 1548 397 1150 1.06 728 330 .943 1.066 .084 .092
12 12613 16777 564 539 12049 16238 13608 17254 581 567 13044 16715 0 0 4037 5804 122 168 100 100 100 100 28287 29759 .742 1.348 1.281 1.336 1.316 1.105 52 400 1.364 .99 90 3590 18390 58 67 302 311 0 11570 372 11199 .929 11899 11528 1.076 .884 -.106 -.178
13 1000 1026 513 473 487 553 897 865 518 477 384 392 0 0 359 416 74 77 100 100 87 90 1040 776 .881 1.136 1.021 1.12 1.091 1.806 32 176 1.155 .86 60 3810 18400 61 67 326 332 0 708 326 381 .783 597 270 1.277 .704 -.353 -.506
14 762 760 510 479 252 281 612 669 514 498 102 190 0 0 305 300 87 104 53 63 46 48 533 292 .897 1.115 1.863 1.301 1.381 2.291 52 412 1.03 .8 90 4040 18390 58 67 347 356 -50 524 330 194 .769 461 131 1.3 1.285 -.379 .361
15 609 487 474 460 135 27 559 462 496 483 85 2 0 0 181 140 167 184 30 13 11 3 162 87 5 .2 .024 .528 .631 3.092 52 412 1.012 .86 90 4270 18390 58 67 370 379 -50 336 317 19 .138 319 1 7.25 .016 -2.858 -5.945
16 772 893 489 459 283 434 710 809 491 461 221 350 0 0 216 221 68 67 75 100 66 100 717 571 .652 1.534 1.584 2.135 1.75 2.337 12 98 .899 .89 50 4490 18390 60 65 394 399 0 616 317 299 1.058 558 241 .946 1.092 .081 .127
17 638 489 618 582 20 -93 561 421 645 605 -57 -161 0 0 246 226 176 190 32 15 9 1 -73 -218 null null null 1.179 1.296 2.446 52 412 1.073 .69 90 1100 18650 84 93 53 62 -50 337 401 -64 null 290 null null null null null
18 625 530 552 529 73 1 569 530 556 528 17 1 0 0 168 101 81 81 38 21 23 7 74 18 73 .014 .059 .851 .991 5.118 52 420 .48 .33 90 1330 18650 84 93 76 85 -50 366 365 1 .009 366 1 105.85 .041 -6.726 -4.624
19 596 547 528 497 68 50 546 495 528 500 18 -2 0 0 231 171 78 80 30 26 17 11 118 16 1.36 .735 null 1.025 1.115 4.224 52 420 .718 .57 90 1560 18650 84 93 99 108 -50 377 343 34 .507 341 null 1.972 null -.98 null
20 800 849 502 469 298 380 757 831 511 477 255 362 0 0 202 199 73 82 87 96 81 84 678 617 .784 1.275 1.42 1.405 1.311 1.948 32 176 1.278 .85 60 1790 18640 85 91 124 130 0 586 323 262 .879 573 250 1.137 .979 -.185 -.031

Total number of rows: 7680

Table truncated, full table size 1847 Kbytes.




Supplementary data files not provided
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