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Sample GSM483 Query DataSets for GSM483
Status Public on Jul 25, 2001
Title G50 genomic DNA vs Tigr/Astra reference
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA, 1ug Astra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 2ug G50 genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Genomic DNA
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.42
Scanning parameters:
Lot batch = hp2030
 
Submission date Jul 25, 2001
Last update date Nov 21, 2005
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 GPL15
Series (2)
GSE6 Genetic diversity among Helicobacter pylori strains
GSE3479 Helicobacter pylori bacterial populations

Data table header descriptions
ID_REF
CH1B_MEAN mean channel 1 background
CH1B_MEDIAN median channel 1 background
CH1D_MEAN difference between CH1I_MEAN and CH1B_MEAN
CH2I_MEAN mean channel 2 signal
CH2D_MEAN difference of CH2I_MEAN and CH2B_MEAN
CH2B_MEAN mean of channel 2 background
CH2B_MEDIAN median of channel 2 background
CH2BN_MEDIAN normalized CH2B_MEDIAN
CH2DN_MEAN normalized CH2D_MEAN
CH2IN_MEAN normalized CH2I_MEAN
CORR simple correlation coefficient of channel 1 and channel 2 pixels
FLAG user defined flag (default=0)
VALUE same as UNF_VALUE but with flagged values removed
PIX_RAT2_MEDIAN
PERGTBCH1I_1SD standard deviation of fraction of pixels greater than CH1B_MEAN
PERGTBCH2I_1SD standard deviation of fraction of pixels greater than CH2B_MEAN
RAT1_MEAN ratio of CH1D_MEAN to CH2D_MEAN
RAT1N_MEAN ratio of CH1DN_MEAN to CH2DN_MEAN
RAT2_MEAN ratio of CH2D_MEAN to CH1D_MEAN
RAT2N_MEAN ratio of CH2DN_MEAN and CH1DN_MEAN
REGR slope of the simple regression line of channel 2 to channel 1 pixels
TOT_BPIX total number of background pixels
TOT_SPIX total number of signal (spot) pixels
TOP vertical, short-axis spot ellipse minimum pixel coordinate
BOT vertical, short-axis spot ellipse maximum pixel coordinate
LEFT horizontal, long-axis spot ellipse minimum pixel coordinate
RIGHT horizontal, long-axis spot ellipse maximum pixel coordinate
UNF_VALUE aka LOG_RAT2N_MEAN, or log2 of ratio of CH2DN_MEAN and CH1DN_MEAN

Data table
ID_REF CH1B_MEAN CH1B_MEDIAN CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2B_MEAN CH2B_MEDIAN CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CORR FLAG VALUE PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH2I_1SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2N_MEAN REGR TOT_BPIX TOT_SPIX TOP BOT LEFT RIGHT UNF_VALUE
1 599 524 640 727 708 1914 1730 .05 0 7.579 0 1 .159 1466 112 36 48 55 67
2 530 521 724 29 709 695 1878 79 1957 -.191 0 6.769 0 8 -.727 1445 112 37 49 74 86
3 570 555 3862 1812 1114 718 698 1886 3011 4897 0 0 -.359 .325 76 61 3.467 1.283 .288 .78 0 1425 225 35 52 99 116 -.359
4 575 560 246 741 51 712 690 1865 138 2003 .206 0 -.834 .591 25 6 4.824 1.783 .207 .561 .101 1504 112 37 49 127 139 -.834
5 567 554 134 719 29 709 690 1865 78 1943 .287 0 -.781 .903 15 8 4.621 1.718 .216 .582 .286 1476 112 37 49 152 164 -.781
6 575 564 3224 1256 555 720 701 1895 1500 3395 .697 0 -1.104 .184 81 50 5.809 2.149 .172 .465 .148 1496 137 35 48 173 186 -1.104
7 567 564 351 780 83 714 697 1884 224 2108 .329 0 -.648 .523 47 10 4.229 1.567 .236 .638 .187 1522 112 38 50 200 212 -.648
8 559 554 134 667 687 673 1819 1803 .229 0 .784 17 5 .219 1509 112 38 50 224 236
9 580 569 2119 1475 829 664 646 1746 2240 3986 .815 0 .08 .424 78 62 2.556 .946 .391 1.057 .358 1499 112 38 50 248 260 .08
10 588 571 218 804 157 663 647 1749 424 2173 .447 0 .96 .932 27 24 1.389 .514 .72 1.945 .405 1455 112 38 50 272 284 .96
11 612 592 239 748 72 686 676 1827 195 2022 .485 0 -.294 .884 29 11 3.319 1.226 .301 .816 .319 1483 112 38 50 296 308 -.294
12 603 580 2210 814 154 674 660 1784 416 2200 .186 0 -2.409 .116 79 22 14.351 5.313 .07 .188 .028 1508 112 39 51 320 332 -2.409
13 543 537 1243 1250 628 637 622 1681 1697 3378 .565 0 .449 .498 91 74 1.979 .732 .505 1.365 .342 1509 112 39 51 344 356 .449
14 521 518 2694 1553 955 618 598 1616 2581 4197 .804 0 -.062 .409 77 65 2.821 1.044 .354 .958 .301 1509 112 39 51 368 380 -.062
15 511 507 216 722 129 601 593 1603 348 1951 .531 0 .688 1.114 27 21 1.674 .621 .597 1.611 .452 1519 112 39 51 392 404 .688
16 504 496 1061 980 398 591 582 1573 1076 2649 .772 0 .02 .448 61 50 2.666 .986 .375 1.014 .327 1504 112 40 52 417 429 .02
17 489 483 2049 1210 633 594 577 1559 1711 3270 .848 0 -.26 .363 67 52 3.237 1.198 .309 .835 .277 1533 112 40 52 441 453 -.26
18 547 536 463 765 59 718 706 1908 160 2068 .532 0 -1.533 .456 43 13 7.847 2.894 .127 .346 .207 1495 112 60 72 55 67 -1.533
19 590 578 2450 1609 895 735 714 1930 2419 4349 .732 0 -.018 .381 90 71 2.737 1.013 .365 .987 .327 1476 112 61 73 79 91 -.018
20 582 579 256 745 51 712 694 1876 138 2014 .285 0 -.891 .748 30 9 5.02 1.855 .199 .539 .168 1450 112 61 73 103 115 -.891

Total number of rows: 4608

Table truncated, full table size 568 Kbytes.




Supplementary data files not provided

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